Gene loci information

Transcript annotation

  • This transcript has been annotated as Clathrin heavy chain.

Parent gene

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_1 g11238 g11238.t1 TTS g11238.t1 14853234 14853234
chr_1 g11238 g11238.t1 isoform g11238.t1 14853845 14861913
chr_1 g11238 g11238.t1 exon g11238.t1.exon1 14853845 14853863
chr_1 g11238 g11238.t1 cds g11238.t1.CDS1 14853845 14853863
chr_1 g11238 g11238.t1 exon g11238.t1.exon2 14853927 14853938
chr_1 g11238 g11238.t1 cds g11238.t1.CDS2 14853927 14853938
chr_1 g11238 g11238.t1 exon g11238.t1.exon3 14853986 14853995
chr_1 g11238 g11238.t1 cds g11238.t1.CDS3 14853986 14853995
chr_1 g11238 g11238.t1 exon g11238.t1.exon4 14854114 14854336
chr_1 g11238 g11238.t1 cds g11238.t1.CDS4 14854114 14854336
chr_1 g11238 g11238.t1 exon g11238.t1.exon5 14854390 14854476
chr_1 g11238 g11238.t1 cds g11238.t1.CDS5 14854390 14854476
chr_1 g11238 g11238.t1 exon g11238.t1.exon6 14854539 14854705
chr_1 g11238 g11238.t1 cds g11238.t1.CDS6 14854539 14854705
chr_1 g11238 g11238.t1 exon g11238.t1.exon7 14854772 14859281
chr_1 g11238 g11238.t1 cds g11238.t1.CDS7 14854772 14859281
chr_1 g11238 g11238.t1 exon g11238.t1.exon8 14861872 14861913
chr_1 g11238 g11238.t1 cds g11238.t1.CDS8 14861872 14861913
chr_1 g11238 g11238.t1 TSS g11238.t1 NA NA

Sequences

>g11238.t1 Gene=g11238 Length=5070
ATGTCTCAGTCATTGCCGATTCGTTTTCAGGAGCATTTGCAGCTCACAAATGTCGGTATT
CAGGCAACATCGATTTCATTTAGTAATCTTACAATGGAATCAGATAAGTTTATCTGCATT
CGAGAAAAAGTTGGAGAAACAGCTCAAGTTGTCATCATTGATATGAGTGATTCTTCAAAT
CCAATTCGACGACCAATTAGCGCTGATTCAGCTATCATGAATCCTGCGAGTAAAGTAATT
GCATTGAAAGCTGCAAAAACTCTTCAAATTTTTAACATCGAGATGAAATCAAAAATGAAG
GCTCACACAATGACTGAGGATGTTGTTTTCTGGAAGTGGATTTCATTAAATACTTTATCA
TTGGTAACTGAAACTTGTGTTTATCATTGGTCAATGGAGGGTGATTCCCAGCCAGTTAAA
ATGTTTGAACGTCATTCGTCACTCAATAGCTGTCAAATCATTAATTATCGCACCGATCCA
AAGCAGCAATGGCTATTACTTATTGGCATTTCAGCACAGCAAAATCGTGTTGTTGGAGCC
ATGCAATTATATTCAGTTGAGAGGAAAGTATCTCAAGCTATTGAAGGTCATGCTGCTGCA
TTTACAACATTCCAGATGGAGGGAAATAAGGAGCCATCAATTATTTTCACTTTTGCTGTG
CGTACACAAACCGGTGGAAAATTGCACATCATCGAAGTTGGAACACCACCTACAGATAAT
CAACCGTTTACAAAGAAAACCGTTGATGTTTTCTTTCCACCTGAAGCGGCTAATGATTTT
CCAGTGGCAATGCAAACATCTCAAAAATATGACGTCATCTACTTGATTACAAAATATGGG
TACATTCATCTTTATGACATTGAAACCGGTACATGTATTTACATGAATCGCATTTCTGCC
GATACTATTTTTGTAACAGCACCACATGATGCTAGTGGTGGTATTATTGGTGTTAACCGT
AAGGGTCAAGTGTTGTCTGTGACAGTCGATGAGGAGCAAATTATTCCTTATATTACTACC
GTTCTTCAAAATCCAGATTTGGCCTTACGCATGGCTGTAAGAAACAATTTGAGCGGGGCT
GAAGATCTTTTTGTGAGAAAGTTCAATCAACTTTTCCAAAACGCTCAATATGCTGAAGCC
GCAAAAGTTGCAGCCGTCGCTCCAAAGGGAATTTTGCGTACACCACAAACTATTCAAAAA
TTCCAACAAGTGCAACCTCCACCGGGCAGCACATCACCACCATTGCTTCAATACTTTGGT
ATTCTCTTAGATCAAGGAAAATTGAATAAATATGAATCACTTGAGCTGTGTCGTCCAGTT
TTATTGCAAGGTCGAATTCAATTGTGTGAGAAATGGTTAAAGGAGCAAAAACTTGAATGC
AGTGAAGAACTTGGTGATTTGGTAAAGCCAACTGATCCAACATTGGCCTTATCTATTTAT
TTACGATCAAATGTCCCAAATAAGGTCATTCAATGTTTTGCTGAGACTGGTCAATTCCAG
AAAATTGTATTGTACGCCAAGAAAGTAAACTACACACCTGATTACATTTTCTTGTTACGT
TCTGTTATGCGCACTAATCCAGAACAAGGTGCAGGTTTCGCTGCTATGCTTGTTGCTGAC
GAAGAACCATTAGCTGACATCAATCAAATTGTTGACATTTTCATGGAACAAAATATGGTT
CAACAATGCACTGCTTTTCTTCTTGATGCACTCAAGCACAATCGACCAACCGAAGGTCCT
TTACAGACACGTCTCTTGGAAATGAACTTGATGTCTGCACCACAAGTTGCTGATGCAATT
TTAGGAAATGCAATGTTCACCCACTATGATCGCGCTCACATCGCACAATTATGTGAAAAA
GCTGGACTTTTACAACGTGCATTAGAACATTACACTGATTTGTATGACATTAAACGTGCT
GTTGTACATACACACTTGTTAAATGGTGATTGGCTTGTTGGTTTCTTTGGCACTCTATCA
GTCGAAGATTCATTGGAATGCTTAAAAGCAATGTTAACAGCTAATATTCGTCAAAATCTT
CAAATTTGTGTTCAAATTGCAACAAAATATCACGAGCAACTAACAACAAAAGCACTCATC
GACTTGTTTGAATCATTTAAGAGCTACGAAGGACTTTTTTATTTCTTGGGATCAATCGTT
AACTTCTCACAAGACTCAGAAGTTCATTTCAAGTACATTCAAGCCGCATGCAAAACAAAT
CAAATTAAAGAGGTGGAGCGCATTTGTCGTGAATCTAATTGCTATCATCCGGAACGTGTC
AAGAACTTTTTGAAGGAAGCCAAATTAACTGATCAACTTCCATTAATTATTGTTTGTGAT
CGATTTGATTTTGTACACGATTTAGTTCTATACTTGTATCGTAACAGTTTACAAAAGTAT
ATCGAGATTTATGTTCAAAAAGTTAATCCTTCACGTTTACCAGTGGTTGTGGGGGGATTG
CTTGATGTCGATTGCTCGGAGGACATTATTAAAAACTTGATTCTCGTCGTTAAGGGACAA
TTTTCAACTGATGAGCTTGTTGAAGAAGTTGAAAAACGAAATAGATTGAAATTGCTTCTA
CCATGGTTGGAATCACGAGTTCATGAAGGTTGTATTGAACCGGCAACACACAATGCTTTA
GCTAAAATTTATATTGATTCAAACAACAATCCCGAGAGGTTCCTTCGTGAAAATCAATTC
TATGACAGTCAAGTTGTTGGAAAATATTGCGAAAAGCGTGATCCACATTTAGCATGTGTT
GCTTATGAAAGAGGTACATGTGATCGAGAACTGATTGCCGTATGTAATGAGAACTCGCTT
TTCAAAACTGAAGCACGTTATTTGGTTAAAAGAAAGGATCCAGAGTTATGGGCTGAGGTT
CTCTCAGAATCAAATCCTTACAAACGTCAACTTATTGATCAAGTCGTTCAAACAGCTCTT
TCTGAAACACAAGATACTGAAGATATTTCTGTTACTGTCAAAGCATTCATGGCTGCCGAT
TTGCCAAATGAATTGATTGAGCTTCTTGAGAAAATTGTCCTCGATTCATCCGTCTTTTCT
GATCACCGCAATTTACAAAATCTTTTGATTTTGACTGCAATTAAGGCCGATTGTACGCGT
GTTATGGATTACATCAATCGTTTAGACAATTACGATGCTCCAGATATTGCAAATATTGCT
ATCAACAGCCACTTATACGAAGAAGCATTTGCAATTTTCAAAAAATTTGAGGTCAATACA
AGCGCTATTCAAGTGCTTATCGAACAATTGAACAATCTCGAGCGTGCATATGAATTTGCA
GAGAGATGCAATGAATCAGCAGTTTGGTCACAACTCGGTCGTGCTCAGCTTCAACAAGGA
TTAGTAAAAGAAGCAATCGATAGTTTTATTAAAGCTGACGATCCATCAGCTTATATTGAT
GTTGTTGATGTTGCAAGTAAGAATGAATCATGGGAGGATCTTGTCAGATATTTGCAAATG
GCACGCAAGAAGGCACGCGAAAGCTATATTGAAAGCGAATTGATTTATGCTTATGCTCGT
ACTGGTCGTTTGGCAGATTTAGAAGAATTCATTAGTGGGCCCAACCACGCAGATATTCAG
AAAATTGGTGATCGTTGCTTTAATGACAAAATGTATGAAGCTGCCAAACTTTTATATAAC
AATGTCAGTAATTTTGCACGATTGGCAATCACATTGGTTCATTTGAAAGAATTCCAAGGA
GCAGTTGATGGTGCTCGTAAAGCAAATTCAACAAGAACATGGAAAGAAGTTTGTTTTGCA
TGTGTAGATTCAGAAGAATTCCGTTTGGCTCAAATGTGTGGTCTTCACATTGTTGTTCAT
GCTGATGAATTGGAAGATTTAATCAACTATTATCAAGATCGTGGATATTTTGAGGAATTG
ATTGGACTTTTGGAAGCAGCTCTTGGCCTTGAACGTGCTCATATGGGTATGTTTACTGAA
TTGGCAATCTTATATTCAAAATACAAGCCAGCCAAGATGCGCGAACATCTCGAATTGTTT
TGGTCACGTGTCAATATTCCAAAAGTCTTGCGTGCAGCTGAATCAGCTCATTTGTGGAGT
GAATTGGTGTTCCTTTATGATAAATACGAAGAATACGATAATGCAGTGTTAGCAATGATG
GCACATCCAACTGAAGCTTGGCGTGAAGGGCACTTTAAAGATATTATCACAAAAGTGGCA
AACATTGAGCTCTACTATAAAGCAATCCAATTCTACTTGGATTATAAACCACTCTTATTG
AATGACCTGCTTTTAGTTCTTACTCCACGTATGGATCATACTAGATCTGTCAACTTTTTC
ACAAAAACTGGACATCTTCAACTCGTCAAACCTTACTTGCGATCAGTTCAAAGTTTGAAT
AACAAAGCCATTAATGAGGCACTAAATGGACTTTTAATCGACGAAGAAGACTACCAAGGA
TTGAGGACATCAATTGATGCATTCGACAACTTTGACAACATTGCATTAGCACAGAAACTT
GAGAAACACGAATTAACAGAATTCCGTCGTATTGCTGCTTATCTATACAAAGGTAACAAT
CGCTGGAAGCAAAGTGTTGAATTATGTAAGAAAGATCGCCTATTCAAAGACGCAATGGAA
TATGCAGCTGAATCACACCAACAGGAAATTGCTGAAGAACTTTTGCAGTGGTTCCTTGAA
CGTGGCGCTAAAGATTGTTTCGCTGCATGCCTCTATACTTGCTATGATCTTTTAAGACCT
GATGTTATTCTCGAATTAGCATGGAGACACAATATTATGGACTTTGCAATGCCCTTCATG
ATCAATGTGATAAGGGAATATACAACAAAAGTAGATAAACTTGAAGCAGCAAATGCCGAA
AGAGAGAAAGAGGGTGAAAATACAGAGCATAAGCCAATAATTATGCAGGAACCACAATTG
ATGTTGACAGCAGGTCCTGCTTATCAATATGGTGCTCCTCAATACGCTCCAAATATTCCA
AATATGCCATATGGAGCAGCGCCGCCAGCGAATCCATACCAAAACTATGGTGGTGGCATC
ATTATAAATTGCGATTTTATTGTTATGTAA

>g11238.t1 Gene=g11238 Length=1689
MSQSLPIRFQEHLQLTNVGIQATSISFSNLTMESDKFICIREKVGETAQVVIIDMSDSSN
PIRRPISADSAIMNPASKVIALKAAKTLQIFNIEMKSKMKAHTMTEDVVFWKWISLNTLS
LVTETCVYHWSMEGDSQPVKMFERHSSLNSCQIINYRTDPKQQWLLLIGISAQQNRVVGA
MQLYSVERKVSQAIEGHAAAFTTFQMEGNKEPSIIFTFAVRTQTGGKLHIIEVGTPPTDN
QPFTKKTVDVFFPPEAANDFPVAMQTSQKYDVIYLITKYGYIHLYDIETGTCIYMNRISA
DTIFVTAPHDASGGIIGVNRKGQVLSVTVDEEQIIPYITTVLQNPDLALRMAVRNNLSGA
EDLFVRKFNQLFQNAQYAEAAKVAAVAPKGILRTPQTIQKFQQVQPPPGSTSPPLLQYFG
ILLDQGKLNKYESLELCRPVLLQGRIQLCEKWLKEQKLECSEELGDLVKPTDPTLALSIY
LRSNVPNKVIQCFAETGQFQKIVLYAKKVNYTPDYIFLLRSVMRTNPEQGAGFAAMLVAD
EEPLADINQIVDIFMEQNMVQQCTAFLLDALKHNRPTEGPLQTRLLEMNLMSAPQVADAI
LGNAMFTHYDRAHIAQLCEKAGLLQRALEHYTDLYDIKRAVVHTHLLNGDWLVGFFGTLS
VEDSLECLKAMLTANIRQNLQICVQIATKYHEQLTTKALIDLFESFKSYEGLFYFLGSIV
NFSQDSEVHFKYIQAACKTNQIKEVERICRESNCYHPERVKNFLKEAKLTDQLPLIIVCD
RFDFVHDLVLYLYRNSLQKYIEIYVQKVNPSRLPVVVGGLLDVDCSEDIIKNLILVVKGQ
FSTDELVEEVEKRNRLKLLLPWLESRVHEGCIEPATHNALAKIYIDSNNNPERFLRENQF
YDSQVVGKYCEKRDPHLACVAYERGTCDRELIAVCNENSLFKTEARYLVKRKDPELWAEV
LSESNPYKRQLIDQVVQTALSETQDTEDISVTVKAFMAADLPNELIELLEKIVLDSSVFS
DHRNLQNLLILTAIKADCTRVMDYINRLDNYDAPDIANIAINSHLYEEAFAIFKKFEVNT
SAIQVLIEQLNNLERAYEFAERCNESAVWSQLGRAQLQQGLVKEAIDSFIKADDPSAYID
VVDVASKNESWEDLVRYLQMARKKARESYIESELIYAYARTGRLADLEEFISGPNHADIQ
KIGDRCFNDKMYEAAKLLYNNVSNFARLAITLVHLKEFQGAVDGARKANSTRTWKEVCFA
CVDSEEFRLAQMCGLHIVVHADELEDLINYYQDRGYFEELIGLLEAALGLERAHMGMFTE
LAILYSKYKPAKMREHLELFWSRVNIPKVLRAAESAHLWSELVFLYDKYEEYDNAVLAMM
AHPTEAWREGHFKDIITKVANIELYYKAIQFYLDYKPLLLNDLLLVLTPRMDHTRSVNFF
TKTGHLQLVKPYLRSVQSLNNKAINEALNGLLIDEEDYQGLRTSIDAFDNFDNIALAQKL
EKHELTEFRRIAAYLYKGNNRWKQSVELCKKDRLFKDAMEYAAESHQQEIAEELLQWFLE
RGAKDCFAACLYTCYDLLRPDVILELAWRHNIMDFAMPFMINVIREYTTKVDKLEAANAE
REKEGENTEHKPIIMQEPQLMLTAGPAYQYGAPQYAPNIPNMPYGAAPPANPYQNYGGGI
IINCDFIVM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
29 g11238.t1 Coils Coil Coil 1083 1103 -
28 g11238.t1 Coils Coil Coil 1604 1631 -
22 g11238.t1 Gene3D G3DSA:2.130.10.110 - 1 364 1.3E-184
23 g11238.t1 Gene3D G3DSA:1.25.40.10 - 445 772 7.3E-20
25 g11238.t1 Gene3D G3DSA:1.25.40.10 - 889 1040 2.0E-6
24 g11238.t1 Gene3D G3DSA:1.25.40.10 - 1041 1183 1.1E-39
26 g11238.t1 Gene3D G3DSA:1.25.40.10 - 1184 1523 2.9E-166
27 g11238.t1 Gene3D G3DSA:1.25.40.730 - 1529 1625 2.3E-44
13 g11238.t1 PANTHER PTHR10292:SF7 CLATHRIN HEAVY CHAIN 1 4 1651 0.0
14 g11238.t1 PANTHER PTHR10292 CLATHRIN HEAVY CHAIN RELATED 4 1651 0.0
30 g11238.t1 PIRSF PIRSF002290 CHC 2 1669 0.0
4 g11238.t1 Pfam PF01394 Clathrin propeller repeat 149 187 1.2E-8
2 g11238.t1 Pfam PF01394 Clathrin propeller repeat 257 288 2.4E-6
3 g11238.t1 Pfam PF01394 Clathrin propeller repeat 296 330 9.9E-6
1 g11238.t1 Pfam PF09268 Clathrin, heavy-chain linker 331 354 9.9E-13
12 g11238.t1 Pfam PF13838 Clathrin-H-link 356 422 5.4E-29
9 g11238.t1 Pfam PF00637 Region in Clathrin and VPS 543 679 1.2E-24
8 g11238.t1 Pfam PF00637 Region in Clathrin and VPS 690 827 4.0E-23
5 g11238.t1 Pfam PF00637 Region in Clathrin and VPS 843 970 3.9E-29
11 g11238.t1 Pfam PF00637 Region in Clathrin and VPS 980 1120 7.5E-33
6 g11238.t1 Pfam PF00637 Region in Clathrin and VPS 1130 1268 3.9E-29
7 g11238.t1 Pfam PF00637 Region in Clathrin and VPS 1277 1418 2.5E-32
10 g11238.t1 Pfam PF00637 Region in Clathrin and VPS 1426 1564 2.2E-29
42 g11238.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 538 684 41.657
44 g11238.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 687 829 37.108
43 g11238.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 834 973 37.601
41 g11238.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 980 1125 42.872
39 g11238.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 1129 1270 39.128
40 g11238.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 1275 1421 40.926
38 g11238.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 1424 1567 36.09
35 g11238.t1 SMART SM00299 CLH_2 538 680 8.0E-39
37 g11238.t1 SMART SM00299 CLH_2 687 829 1.6E-42
36 g11238.t1 SMART SM00299 CLH_2 834 973 3.6E-42
34 g11238.t1 SMART SM00299 CLH_2 980 1125 3.1E-38
32 g11238.t1 SMART SM00299 CLH_2 1129 1270 3.5E-36
33 g11238.t1 SMART SM00299 CLH_2 1275 1421 1.5E-40
31 g11238.t1 SMART SM00299 CLH_2 1424 1583 2.8E-39
21 g11238.t1 SUPERFAMILY SSF50989 Clathrin heavy-chain terminal domain 4 330 1.27E-146
15 g11238.t1 SUPERFAMILY SSF48371 ARM repeat 332 488 2.24E-55
19 g11238.t1 SUPERFAMILY SSF48371 ARM repeat 446 780 7.19E-99
20 g11238.t1 SUPERFAMILY SSF48371 ARM repeat 804 889 1.04E-5
17 g11238.t1 SUPERFAMILY SSF48371 ARM repeat 888 1066 1.27E-40
16 g11238.t1 SUPERFAMILY SSF48371 ARM repeat 1038 1181 4.89E-29
18 g11238.t1 SUPERFAMILY SSF48371 ARM repeat 1184 1517 4.43E-115

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:0030130 clathrin coat of trans-Golgi network vesicle CC
GO:0016192 vesicle-mediated transport BP
GO:0006886 intracellular protein transport BP
GO:0030132 clathrin coat of coated pit CC
GO:0005515 protein binding MF
GO:0005198 structural molecule activity MF
GO:0032051 clathrin light chain binding MF
GO:0071439 clathrin complex CC

KEGG

Orthology

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.

Raw TPM values