General information for g1374.t1
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.t1 | isoform | g1374.t1 | 10236593 | 10242778 |
| chr_3 | g1374 | g1374.t1 | exon | g1374.t1.exon1 | 10236593 | 10236841 |
| chr_3 | g1374 | g1374.t1 | cds | g1374.t1.CDS1 | 10236593 | 10236841 |
| chr_3 | g1374 | g1374.t1 | exon | g1374.t1.exon2 | 10237273 | 10237925 |
| chr_3 | g1374 | g1374.t1 | cds | g1374.t1.CDS2 | 10237273 | 10237925 |
| chr_3 | g1374 | g1374.t1 | exon | g1374.t1.exon3 | 10237981 | 10238729 |
| chr_3 | g1374 | g1374.t1 | cds | g1374.t1.CDS3 | 10237981 | 10238729 |
| chr_3 | g1374 | g1374.t1 | exon | g1374.t1.exon4 | 10238786 | 10238883 |
| chr_3 | g1374 | g1374.t1 | cds | g1374.t1.CDS4 | 10238786 | 10238883 |
| chr_3 | g1374 | g1374.t1 | exon | g1374.t1.exon5 | 10239320 | 10239528 |
| chr_3 | g1374 | g1374.t1 | cds | g1374.t1.CDS5 | 10239320 | 10239528 |
| chr_3 | g1374 | g1374.t1 | exon | g1374.t1.exon6 | 10239582 | 10240353 |
| chr_3 | g1374 | g1374.t1 | cds | g1374.t1.CDS6 | 10239582 | 10240353 |
| chr_3 | g1374 | g1374.t1 | exon | g1374.t1.exon7 | 10242641 | 10242778 |
| chr_3 | g1374 | g1374.t1 | cds | g1374.t1.CDS7 | 10242641 | 10242778 |
| chr_3 | g1374 | g1374.t1 | TSS | g1374.t1 | 10243197 | 10243197 |
| chr_3 | g1374 | g1374.t1 | TTS | g1374.t1 | NA | NA |
Sequences
>g1374.t1 Gene=g1374 Length=2868
ATGATGAATTCACATCAAGGCAATCAAGGGAATTCATCCTCAATAGGAACTTATCAATAT
CAAATTGGTGATCAAGTGCTAGAAATTCCATCAAATATCAACTATCAATTGGAAAATATC
ATTGCATCAGGTGGTGGTGTGCAATACATTCTTTCCGATGGCTCAATATTGGTGCAAAAG
GAGATCAAGAAGGATAGTAATAAAAATAATTATCGACGAATGATTGTCGTGAATCAACAG
GATTTGACACAAGCAGCAGCAGCAAATACAACGACAAATACAACGCAAAGTGTTCCAGCT
ATTACACAGCAAAGAATTATTACACAACAAATACCGACAAATGCGAATGGAACAATTGAG
ACAGCAAGAAGCACAGCAGTAAATGCAGCACAAAATCGAAATAATGCGACGCAAGTAATT
ACACCAATGGGACCTTTGACCCTCACGCCCGATGAGTACAATGAGTTGATGCAACGTCGT
ATGCAAAAGCAAGCTCAAGTTGAAGCTGAAGCACAAAGACAAGCACAGCAAGAAGCTCAA
CAGCGTGCTCAACAAGAAGCACAGCAGCGTGCACAACAACAACAGCAGCAACAATTACAT
CAACAGCAAATGCAAGATCATCAAAATATTGCCGTACAAGTGCAAAAAATTGTGCAATCA
TTGGAAGAAGAAGTTGATGGTAAAAAAGACGATGATGATATAGAAATGCAATTGATTGCA
CCAAAAATGGAAGTTACTGACGGTAGTGTACACAGTGAAGGTACATCATCACAAGATCAT
CAACGTCGACATTCGAAACATCAAGAAAGTGGCGAAGGAAAAGGTGCCGGTCGACCATTT
GCATGTGAGCAATGCAATAAAAAATTTCTTCTAAAACATCATTTGACAACGCATTCTCGT
GTTCATACAGGTAATACAAATTCAACAGGTGAACGTCCGCATGTATGCATTCATTGTGGC
AAAGATTTTGCTCATAAACATTGCCTTAATACCCACTTGTTGCTTCATTCTACTGAAAGA
CCTTACCAATGTACAGAATGTAAAAAATGCTTCACACTCAAGCATCATCTTTTGACACAT
TCACGAGTTCATTCAAGAGATAGACCTTTTGTTTGTCAAGAATGTGGAAAGACATTTTCA
TTGAAGCGACATCTTGTTACACATATGAAGTTTCATGCTGGTGAACGTCCGTATGTTTGT
GAGACATGCGGTGAAAGTTTTGCACAAGAGCAACATTTGGTAATGCACTCACGTTTTCAT
GGTAGTGTAGATCCATTTGTATGTCAGGACTGTGGCGCATCATTCCCAAGAAAATTCCAG
CTAGTTAATCATGGCAAGCTTCATGGACGTTTGCCACATGAATGTACAGTTTGTGGTCAA
GAATTCCTACAAAAGCGAACGCTTATTGCTCATATGCGACAACATACGGACGCACCACAT
GTTTGTCTTGAATGTTCTGAAGGATTTAGAACAAAATCAGAACTTACAGCACATGGTCGA
ATAGTTCATAATATTCAACCTCCAGTAAGGCAGAAACATGCATCATCAACTACAACAAGT
CGTAATCAACAACAACTTGAACAGCAACAACAGCAAGAAATTGAAGATGAACAGGAGCAG
CAACAACAAGTTCATTATTTGAAACAAGAACAGCCACAATATGAAACAATTCAATTACAA
GATCATCAAAATTATCAAATTATGGTGCCAACTGCAAGTCCATCAACAGTCGAACATAAA
ACGATAAGAATTCAACAACAACAACCGCAACAGCAAAATGTGCAAAGTCAACACATTTGC
ACGCAATGTGGCAGCTGTTTCAATAATCGCGAGGCATTGAATTTGCATTTAAGATTACAT
ACTGGTGACAAAAGTCTAATGACCGATTTATGTGCACTCACGGCAGCTATTCCTGGTCAT
ATTTTTCAAAGTGGAAATGCTTATATTGAAATTGATGGTGGAAAATATAATATAACAAAT
GGTACTACATTGATGGCAAATACAGGTGGTTCATCACCAGTTCCAGTTCAAATAATCACA
TCAGCAAATGGACAACAAGTAATTGAACAAGTCCAGAGTATTTCGCCATCATTAATTCAA
CAGCAGCATAATCAACATGTTACACAACAAGAAGTTCAAATCGCACAACAACAAGGTCAA
ATTGTTTACACAACAGTGCCTCAAGATTCACCACATACACAAACTGTTCTCGTTCAACAA
CAGCAGCATCAACAGACTCAACCTCAACAACAGCAACAACCACAACAGCAAGTAATTGTT
CATCATCATCAGCCACATCAGCCAAAACCAAAATCACATTTTTGTCAACATTGTCAAAAA
GGTTTTGCTAATAAACATGGCTTGCAACTTCATAATAAACGTCATCCAAATGGCGAATGC
ACAGTTCGTTCTCATGTTTGCAATGAATGCAATCGTGCATTTTTCCAGAAAAATCATCTT
CTATTACATCAACGTCAACATATGGAACAGCAAAGAGGTCAAGGTTTAGTGGCACAAAAT
GATGAAAAAGATGCAATTGGTGATGGTGAAAGAACAAATGGACAGGAACAAGAGCAAGAT
GTTGAAATTGGTGGTGTTGATGAAATTGAAAATCAACAGAAGGTCATTGCAATTGGAAGC
GAAGATGAAACGCAAAAGAGCCAAAAAGAAGTCAACCAAGATGAGGCAAATGTGACAATG
AATGAACATCAATCAAGCGAGTTACGAACGCAAAACGTCATCGTTAGCAACAACAACAAC
AACAATAACATTGAGAATGATGACAAGACAGTAAAAGATGGATCTATAGAAAATGTTCAA
ATTGCAACGACAAACGAAAATGGCGGCTCTTCCATGGAACAGGAATAA
>g1374.t1 Gene=g1374 Length=955
MMNSHQGNQGNSSSIGTYQYQIGDQVLEIPSNINYQLENIIASGGGVQYILSDGSILVQK
EIKKDSNKNNYRRMIVVNQQDLTQAAAANTTTNTTQSVPAITQQRIITQQIPTNANGTIE
TARSTAVNAAQNRNNATQVITPMGPLTLTPDEYNELMQRRMQKQAQVEAEAQRQAQQEAQ
QRAQQEAQQRAQQQQQQQLHQQQMQDHQNIAVQVQKIVQSLEEEVDGKKDDDDIEMQLIA
PKMEVTDGSVHSEGTSSQDHQRRHSKHQESGEGKGAGRPFACEQCNKKFLLKHHLTTHSR
VHTGNTNSTGERPHVCIHCGKDFAHKHCLNTHLLLHSTERPYQCTECKKCFTLKHHLLTH
SRVHSRDRPFVCQECGKTFSLKRHLVTHMKFHAGERPYVCETCGESFAQEQHLVMHSRFH
GSVDPFVCQDCGASFPRKFQLVNHGKLHGRLPHECTVCGQEFLQKRTLIAHMRQHTDAPH
VCLECSEGFRTKSELTAHGRIVHNIQPPVRQKHASSTTTSRNQQQLEQQQQQEIEDEQEQ
QQQVHYLKQEQPQYETIQLQDHQNYQIMVPTASPSTVEHKTIRIQQQQPQQQNVQSQHIC
TQCGSCFNNREALNLHLRLHTGDKSLMTDLCALTAAIPGHIFQSGNAYIEIDGGKYNITN
GTTLMANTGGSSPVPVQIITSANGQQVIEQVQSISPSLIQQQHNQHVTQQEVQIAQQQGQ
IVYTTVPQDSPHTQTVLVQQQQHQQTQPQQQQQPQQQVIVHHHQPHQPKPKSHFCQHCQK
GFANKHGLQLHNKRHPNGECTVRSHVCNECNRAFFQKNHLLLHQRQHMEQQRGQGLVAQN
DEKDAIGDGERTNGQEQEQDVEIGGVDEIENQQKVIAIGSEDETQKSQKEVNQDEANVTM
NEHQSSELRTQNVIVSNNNNNNNIENDDKTVKDGSIENVQIATTNENGGSSMEQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 29 | g1374.t1 | Coils | Coil | Coil | 153 | 197 | - |
| 28 | g1374.t1 | Coils | Coil | Coil | 204 | 231 | - |
| 30 | g1374.t1 | Coils | Coil | Coil | 520 | 543 | - |
| 22 | g1374.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 278 | 309 | 1.5E-8 |
| 27 | g1374.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 310 | 337 | 1.7E-9 |
| 25 | g1374.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 338 | 367 | 2.1E-9 |
| 20 | g1374.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 368 | 395 | 6.2E-12 |
| 24 | g1374.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 396 | 449 | 1.0E-15 |
| 26 | g1374.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 450 | 518 | 2.1E-12 |
| 21 | g1374.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 575 | 643 | 8.8E-7 |
| 23 | g1374.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 757 | 840 | 7.5E-8 |
| 53 | g1374.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 166 | 192 | - |
| 52 | g1374.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 243 | 277 | - |
| 56 | g1374.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 256 | 273 | - |
| 58 | g1374.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 506 | 540 | - |
| 54 | g1374.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 509 | 537 | - |
| 55 | g1374.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 733 | 762 | - |
| 59 | g1374.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 733 | 764 | - |
| 60 | g1374.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 881 | 935 | - |
| 57 | g1374.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 891 | 925 | - |
| 8 | g1374.t1 | PANTHER | PTHR24388:SF82 | ZINC FINGER PROTEIN 648-RELATED | 258 | 392 | 2.4E-111 |
| 12 | g1374.t1 | PANTHER | PTHR24388 | ZINC FINGER PROTEIN | 258 | 392 | 2.4E-111 |
| 6 | g1374.t1 | PANTHER | PTHR24388:SF82 | ZINC FINGER PROTEIN 648-RELATED | 278 | 449 | 2.4E-111 |
| 10 | g1374.t1 | PANTHER | PTHR24388 | ZINC FINGER PROTEIN | 278 | 449 | 2.4E-111 |
| 5 | g1374.t1 | PANTHER | PTHR24388:SF82 | ZINC FINGER PROTEIN 648-RELATED | 357 | 503 | 2.4E-111 |
| 9 | g1374.t1 | PANTHER | PTHR24388 | ZINC FINGER PROTEIN | 357 | 503 | 2.4E-111 |
| 7 | g1374.t1 | PANTHER | PTHR24388:SF82 | ZINC FINGER PROTEIN 648-RELATED | 514 | 828 | 2.4E-111 |
| 11 | g1374.t1 | PANTHER | PTHR24388 | ZINC FINGER PROTEIN | 514 | 828 | 2.4E-111 |
| 4 | g1374.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 370 | 392 | 8.5E-4 |
| 1 | g1374.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 398 | 420 | 0.013 |
| 2 | g1374.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 426 | 448 | 4.6E-4 |
| 3 | g1374.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 480 | 503 | 0.0073 |
| 39 | g1374.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 282 | 302 | - |
| 40 | g1374.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 316 | 336 | - |
| 32 | g1374.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 344 | 364 | - |
| 35 | g1374.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 372 | 392 | - |
| 33 | g1374.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 400 | 420 | - |
| 37 | g1374.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 428 | 448 | - |
| 34 | g1374.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 455 | 475 | - |
| 31 | g1374.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 482 | 503 | - |
| 36 | g1374.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 600 | 620 | - |
| 38 | g1374.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 807 | 827 | - |
| 65 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 280 | 307 | 13.38 |
| 62 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 314 | 341 | 13.027 |
| 71 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 342 | 369 | 14.981 |
| 69 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 370 | 397 | 16.498 |
| 68 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 398 | 425 | 13.256 |
| 64 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 426 | 448 | 10.596 |
| 66 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 453 | 480 | 11.448 |
| 70 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 480 | 508 | 11.614 |
| 63 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 598 | 625 | 13.568 |
| 61 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 773 | 795 | 9.265 |
| 67 | g1374.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 805 | 832 | 12.175 |
| 50 | g1374.t1 | SMART | SM00355 | c2h2final6 | 280 | 302 | 0.42 |
| 46 | g1374.t1 | SMART | SM00355 | c2h2final6 | 314 | 336 | 3.9 |
| 49 | g1374.t1 | SMART | SM00355 | c2h2final6 | 342 | 364 | 0.3 |
| 47 | g1374.t1 | SMART | SM00355 | c2h2final6 | 370 | 392 | 0.0023 |
| 48 | g1374.t1 | SMART | SM00355 | c2h2final6 | 398 | 420 | 0.022 |
| 44 | g1374.t1 | SMART | SM00355 | c2h2final6 | 426 | 448 | 0.3 |
| 43 | g1374.t1 | SMART | SM00355 | c2h2final6 | 453 | 475 | 0.0023 |
| 45 | g1374.t1 | SMART | SM00355 | c2h2final6 | 480 | 503 | 3.0 |
| 41 | g1374.t1 | SMART | SM00355 | c2h2final6 | 598 | 620 | 0.0037 |
| 42 | g1374.t1 | SMART | SM00355 | c2h2final6 | 773 | 795 | 0.51 |
| 51 | g1374.t1 | SMART | SM00355 | c2h2final6 | 805 | 827 | 0.034 |
| 15 | g1374.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 278 | 304 | 6.43E-7 |
| 19 | g1374.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 309 | 360 | 1.03E-11 |
| 18 | g1374.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 351 | 407 | 7.28E-18 |
| 14 | g1374.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 392 | 444 | 3.37E-14 |
| 13 | g1374.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 449 | 498 | 4.41E-10 |
| 17 | g1374.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 597 | 635 | 1.29E-6 |
| 16 | g1374.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 771 | 827 | 2.71E-7 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
