General information for g1374.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histone-lysine N-methyltransferase PRDM9.
Parent gene
- The parent gene g1374 is located on chr_3: 10242633..10242778 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g1374 | g1374.t2 | isoform | g1374.t2 | 10236593 | 10242778 |
| chr_3 | g1374 | g1374.t2 | exon | g1374.t2.exon1 | 10236593 | 10236841 |
| chr_3 | g1374 | g1374.t2 | cds | g1374.t2.CDS1 | 10236593 | 10236841 |
| chr_3 | g1374 | g1374.t2 | exon | g1374.t2.exon2 | 10237273 | 10237925 |
| chr_3 | g1374 | g1374.t2 | cds | g1374.t2.CDS2 | 10237273 | 10237925 |
| chr_3 | g1374 | g1374.t2 | exon | g1374.t2.exon3 | 10237981 | 10238729 |
| chr_3 | g1374 | g1374.t2 | cds | g1374.t2.CDS3 | 10237981 | 10238729 |
| chr_3 | g1374 | g1374.t2 | exon | g1374.t2.exon4 | 10238786 | 10238883 |
| chr_3 | g1374 | g1374.t2 | cds | g1374.t2.CDS4 | 10238786 | 10238883 |
| chr_3 | g1374 | g1374.t2 | exon | g1374.t2.exon5 | 10239320 | 10239510 |
| chr_3 | g1374 | g1374.t2 | cds | g1374.t2.CDS5 | 10239320 | 10239510 |
| chr_3 | g1374 | g1374.t2 | exon | g1374.t2.exon6 | 10239582 | 10240353 |
| chr_3 | g1374 | g1374.t2 | cds | g1374.t2.CDS6 | 10239582 | 10240353 |
| chr_3 | g1374 | g1374.t2 | exon | g1374.t2.exon7 | 10242641 | 10242778 |
| chr_3 | g1374 | g1374.t2 | cds | g1374.t2.CDS7 | 10242641 | 10242778 |
| chr_3 | g1374 | g1374.t2 | TSS | g1374.t2 | 10243197 | 10243197 |
| chr_3 | g1374 | g1374.t2 | TTS | g1374.t2 | NA | NA |
Sequences
>g1374.t2 Gene=g1374 Length=2850
ATGATGAATTCACATCAAGGCAATCAAGGGAATTCATCCTCAATAGGAACTTATCAATAT
CAAATTGGTGATCAAGTGCTAGAAATTCCATCAAATATCAACTATCAATTGGAAAATATC
ATTGCATCAGGTGGTGGTGTGCAATACATTCTTTCCGATGGCTCAATATTGGTGCAAAAG
GAGATCAAGAAGGATAGTAATAAAAATAATTATCGACGAATGATTGTCGTGAATCAACAG
GATTTGACACAAGCAGCAGCAGCAAATACAACGACAAATACAACGCAAAGTGTTCCAGCT
ATTACACAGCAAAGAATTATTACACAACAAATACCGACAAATGCGAATGGAACAATTGAG
ACAGCAAGAAGCACAGCAGTAAATGCAGCACAAAATCGAAATAATGCGACGCAAGTAATT
ACACCAATGGGACCTTTGACCCTCACGCCCGATGAGTACAATGAGTTGATGCAACGTCGT
ATGCAAAAGCAAGCTCAAGTTGAAGCTGAAGCACAAAGACAAGCACAGCAAGAAGCTCAA
CAGCGTGCTCAACAAGAAGCACAGCAGCGTGCACAACAACAACAGCAGCAACAATTACAT
CAACAGCAAATGCAAGATCATCAAAATATTGCCGTACAAGTGCAAAAAATTGTGCAATCA
TTGGAAGAAGAAGTTGATGGTAAAAAAGACGATGATGATATAGAAATGCAATTGATTGCA
CCAAAAATGGAAGTTACTGACGGTAGTGTACACAGTGAAGGTACATCATCACAAGATCAT
CAACGTCGACATTCGAAACATCAAGAAAGTGGCGAAGGAAAAGGTGCCGGTCGACCATTT
GCATGTGAGCAATGCAATAAAAAATTTCTTCTAAAACATCATTTGACAACGCATTCTCGT
GTTCATACAGGTGAACGTCCGCATGTATGCATTCATTGTGGCAAAGATTTTGCTCATAAA
CATTGCCTTAATACCCACTTGTTGCTTCATTCTACTGAAAGACCTTACCAATGTACAGAA
TGTAAAAAATGCTTCACACTCAAGCATCATCTTTTGACACATTCACGAGTTCATTCAAGA
GATAGACCTTTTGTTTGTCAAGAATGTGGAAAGACATTTTCATTGAAGCGACATCTTGTT
ACACATATGAAGTTTCATGCTGGTGAACGTCCGTATGTTTGTGAGACATGCGGTGAAAGT
TTTGCACAAGAGCAACATTTGGTAATGCACTCACGTTTTCATGGTAGTGTAGATCCATTT
GTATGTCAGGACTGTGGCGCATCATTCCCAAGAAAATTCCAGCTAGTTAATCATGGCAAG
CTTCATGGACGTTTGCCACATGAATGTACAGTTTGTGGTCAAGAATTCCTACAAAAGCGA
ACGCTTATTGCTCATATGCGACAACATACGGACGCACCACATGTTTGTCTTGAATGTTCT
GAAGGATTTAGAACAAAATCAGAACTTACAGCACATGGTCGAATAGTTCATAATATTCAA
CCTCCAGTAAGGCAGAAACATGCATCATCAACTACAACAAGTCGTAATCAACAACAACTT
GAACAGCAACAACAGCAAGAAATTGAAGATGAACAGGAGCAGCAACAACAAGTTCATTAT
TTGAAACAAGAACAGCCACAATATGAAACAATTCAATTACAAGATCATCAAAATTATCAA
ATTATGGTGCCAACTGCAAGTCCATCAACAGTCGAACATAAAACGATAAGAATTCAACAA
CAACAACCGCAACAGCAAAATGTGCAAAGTCAACACATTTGCACGCAATGTGGCAGCTGT
TTCAATAATCGCGAGGCATTGAATTTGCATTTAAGATTACATACTGGTGACAAAAGTCTA
ATGACCGATTTATGTGCACTCACGGCAGCTATTCCTGGTCATATTTTTCAAAGTGGAAAT
GCTTATATTGAAATTGATGGTGGAAAATATAATATAACAAATGGTACTACATTGATGGCA
AATACAGGTGGTTCATCACCAGTTCCAGTTCAAATAATCACATCAGCAAATGGACAACAA
GTAATTGAACAAGTCCAGAGTATTTCGCCATCATTAATTCAACAGCAGCATAATCAACAT
GTTACACAACAAGAAGTTCAAATCGCACAACAACAAGGTCAAATTGTTTACACAACAGTG
CCTCAAGATTCACCACATACACAAACTGTTCTCGTTCAACAACAGCAGCATCAACAGACT
CAACCTCAACAACAGCAACAACCACAACAGCAAGTAATTGTTCATCATCATCAGCCACAT
CAGCCAAAACCAAAATCACATTTTTGTCAACATTGTCAAAAAGGTTTTGCTAATAAACAT
GGCTTGCAACTTCATAATAAACGTCATCCAAATGGCGAATGCACAGTTCGTTCTCATGTT
TGCAATGAATGCAATCGTGCATTTTTCCAGAAAAATCATCTTCTATTACATCAACGTCAA
CATATGGAACAGCAAAGAGGTCAAGGTTTAGTGGCACAAAATGATGAAAAAGATGCAATT
GGTGATGGTGAAAGAACAAATGGACAGGAACAAGAGCAAGATGTTGAAATTGGTGGTGTT
GATGAAATTGAAAATCAACAGAAGGTCATTGCAATTGGAAGCGAAGATGAAACGCAAAAG
AGCCAAAAAGAAGTCAACCAAGATGAGGCAAATGTGACAATGAATGAACATCAATCAAGC
GAGTTACGAACGCAAAACGTCATCGTTAGCAACAACAACAACAACAATAACATTGAGAAT
GATGACAAGACAGTAAAAGATGGATCTATAGAAAATGTTCAAATTGCAACGACAAACGAA
AATGGCGGCTCTTCCATGGAACAGGAATAA
>g1374.t2 Gene=g1374 Length=949
MMNSHQGNQGNSSSIGTYQYQIGDQVLEIPSNINYQLENIIASGGGVQYILSDGSILVQK
EIKKDSNKNNYRRMIVVNQQDLTQAAAANTTTNTTQSVPAITQQRIITQQIPTNANGTIE
TARSTAVNAAQNRNNATQVITPMGPLTLTPDEYNELMQRRMQKQAQVEAEAQRQAQQEAQ
QRAQQEAQQRAQQQQQQQLHQQQMQDHQNIAVQVQKIVQSLEEEVDGKKDDDDIEMQLIA
PKMEVTDGSVHSEGTSSQDHQRRHSKHQESGEGKGAGRPFACEQCNKKFLLKHHLTTHSR
VHTGERPHVCIHCGKDFAHKHCLNTHLLLHSTERPYQCTECKKCFTLKHHLLTHSRVHSR
DRPFVCQECGKTFSLKRHLVTHMKFHAGERPYVCETCGESFAQEQHLVMHSRFHGSVDPF
VCQDCGASFPRKFQLVNHGKLHGRLPHECTVCGQEFLQKRTLIAHMRQHTDAPHVCLECS
EGFRTKSELTAHGRIVHNIQPPVRQKHASSTTTSRNQQQLEQQQQQEIEDEQEQQQQVHY
LKQEQPQYETIQLQDHQNYQIMVPTASPSTVEHKTIRIQQQQPQQQNVQSQHICTQCGSC
FNNREALNLHLRLHTGDKSLMTDLCALTAAIPGHIFQSGNAYIEIDGGKYNITNGTTLMA
NTGGSSPVPVQIITSANGQQVIEQVQSISPSLIQQQHNQHVTQQEVQIAQQQGQIVYTTV
PQDSPHTQTVLVQQQQHQQTQPQQQQQPQQQVIVHHHQPHQPKPKSHFCQHCQKGFANKH
GLQLHNKRHPNGECTVRSHVCNECNRAFFQKNHLLLHQRQHMEQQRGQGLVAQNDEKDAI
GDGERTNGQEQEQDVEIGGVDEIENQQKVIAIGSEDETQKSQKEVNQDEANVTMNEHQSS
ELRTQNVIVSNNNNNNNIENDDKTVKDGSIENVQIATTNENGGSSMEQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 28 | g1374.t2 | Coils | Coil | Coil | 153 | 197 | - |
| 27 | g1374.t2 | Coils | Coil | Coil | 204 | 231 | - |
| 29 | g1374.t2 | Coils | Coil | Coil | 514 | 537 | - |
| 21 | g1374.t2 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 278 | 305 | 8.4E-11 |
| 26 | g1374.t2 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 306 | 332 | 2.1E-9 |
| 22 | g1374.t2 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 333 | 362 | 4.4E-9 |
| 20 | g1374.t2 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 363 | 389 | 6.4E-12 |
| 25 | g1374.t2 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 390 | 443 | 8.0E-16 |
| 24 | g1374.t2 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 444 | 513 | 1.7E-12 |
| 19 | g1374.t2 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 569 | 637 | 8.7E-7 |
| 23 | g1374.t2 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 751 | 834 | 7.5E-8 |
| 52 | g1374.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 165 | 192 | - |
| 51 | g1374.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 243 | 277 | - |
| 56 | g1374.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 256 | 273 | - |
| 53 | g1374.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 500 | 534 | - |
| 57 | g1374.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 503 | 531 | - |
| 55 | g1374.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 727 | 756 | - |
| 59 | g1374.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 727 | 758 | - |
| 58 | g1374.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 875 | 929 | - |
| 54 | g1374.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 885 | 919 | - |
| 8 | g1374.t2 | PANTHER | PTHR24406:SF10 | REPLICATION INITIATOR 1 | 258 | 442 | 1.1E-101 |
| 12 | g1374.t2 | PANTHER | PTHR24406 | TRANSCRIPTIONAL REPRESSOR CTCFL-RELATED | 258 | 442 | 1.1E-101 |
| 6 | g1374.t2 | PANTHER | PTHR24406:SF10 | REPLICATION INITIATOR 1 | 354 | 506 | 1.1E-101 |
| 10 | g1374.t2 | PANTHER | PTHR24406 | TRANSCRIPTIONAL REPRESSOR CTCFL-RELATED | 354 | 506 | 1.1E-101 |
| 7 | g1374.t2 | PANTHER | PTHR24406:SF10 | REPLICATION INITIATOR 1 | 419 | 627 | 1.1E-101 |
| 11 | g1374.t2 | PANTHER | PTHR24406 | TRANSCRIPTIONAL REPRESSOR CTCFL-RELATED | 419 | 627 | 1.1E-101 |
| 5 | g1374.t2 | PANTHER | PTHR24406:SF10 | REPLICATION INITIATOR 1 | 750 | 824 | 1.1E-101 |
| 9 | g1374.t2 | PANTHER | PTHR24406 | TRANSCRIPTIONAL REPRESSOR CTCFL-RELATED | 750 | 824 | 1.1E-101 |
| 4 | g1374.t2 | Pfam | PF00096 | Zinc finger, C2H2 type | 364 | 386 | 8.5E-4 |
| 3 | g1374.t2 | Pfam | PF00096 | Zinc finger, C2H2 type | 392 | 414 | 0.013 |
| 2 | g1374.t2 | Pfam | PF00096 | Zinc finger, C2H2 type | 420 | 442 | 4.5E-4 |
| 1 | g1374.t2 | Pfam | PF00096 | Zinc finger, C2H2 type | 474 | 497 | 0.0072 |
| 37 | g1374.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 282 | 302 | - |
| 32 | g1374.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 310 | 330 | - |
| 34 | g1374.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 338 | 358 | - |
| 33 | g1374.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 366 | 386 | - |
| 36 | g1374.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 394 | 414 | - |
| 39 | g1374.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 422 | 442 | - |
| 35 | g1374.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 449 | 469 | - |
| 31 | g1374.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 476 | 497 | - |
| 30 | g1374.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 594 | 614 | - |
| 38 | g1374.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 801 | 821 | - |
| 65 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 280 | 307 | 16.165 |
| 67 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 308 | 335 | 13.027 |
| 68 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 336 | 363 | 14.981 |
| 69 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 364 | 391 | 16.498 |
| 63 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 392 | 419 | 13.256 |
| 62 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 420 | 442 | 10.596 |
| 70 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 447 | 474 | 11.448 |
| 61 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 474 | 502 | 11.614 |
| 66 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 592 | 619 | 13.568 |
| 60 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 767 | 789 | 9.265 |
| 64 | g1374.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 799 | 826 | 12.175 |
| 49 | g1374.t2 | SMART | SM00355 | c2h2final6 | 280 | 302 | 0.42 |
| 47 | g1374.t2 | SMART | SM00355 | c2h2final6 | 308 | 330 | 3.9 |
| 40 | g1374.t2 | SMART | SM00355 | c2h2final6 | 336 | 358 | 0.3 |
| 50 | g1374.t2 | SMART | SM00355 | c2h2final6 | 364 | 386 | 0.0023 |
| 44 | g1374.t2 | SMART | SM00355 | c2h2final6 | 392 | 414 | 0.022 |
| 42 | g1374.t2 | SMART | SM00355 | c2h2final6 | 420 | 442 | 0.3 |
| 43 | g1374.t2 | SMART | SM00355 | c2h2final6 | 447 | 469 | 0.0023 |
| 46 | g1374.t2 | SMART | SM00355 | c2h2final6 | 474 | 497 | 3.0 |
| 45 | g1374.t2 | SMART | SM00355 | c2h2final6 | 592 | 614 | 0.0037 |
| 41 | g1374.t2 | SMART | SM00355 | c2h2final6 | 767 | 789 | 0.51 |
| 48 | g1374.t2 | SMART | SM00355 | c2h2final6 | 799 | 821 | 0.034 |
| 15 | g1374.t2 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 277 | 326 | 5.61E-13 |
| 17 | g1374.t2 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 345 | 401 | 5.66E-18 |
| 18 | g1374.t2 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 386 | 438 | 3.78E-14 |
| 16 | g1374.t2 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 443 | 492 | 3.48E-10 |
| 13 | g1374.t2 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 591 | 629 | 1.27E-6 |
| 14 | g1374.t2 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 765 | 821 | 2.54E-7 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003677 | DNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K09228 (KRAB domain-containing zinc finger protein)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
