RetrogeneDB ID: | retro_fcat_1744 | ||
Retrocopy location | Organism: | Cat (Felis catus) | |
| Coordinates: | F1:7867286..7869227(+) | ||
| Located in intron of: | ENSFCAG00000013336 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CHM | ||
| Ensembl ID: | ENSFCAG00000030652 | ||
| Aliases: | None | ||
| Description: | choroideremia (Rab escort protein 1) [Source:HGNC Symbol;Acc:1940] |
Retrocopy-Parental alignment summary:
>retro_fcat_1744
ATGGCGGACAGTCTCCCCACAGAATTCGATGTGATCATAATAGGGACAGGTCTGCCTGAATCCATCCTTGCAGCTGCGTG
TTCAAGAAGTGGTCAGAGGGTTCTGCATCTCGATTCAAGAAGCTACTATGGAGGAAACTGGGCAAGTTTCAACTTTTCAG
GATTGCTCTCCTGGTTGAAGGAGTACCAGCAAAAGAGTGATGTTGCAGAAGAAAGTACTGCCTCGTGGCAAGGCCTGATT
CATGAAACAGAAGAAGCCATCACTCTGCGCAAGACGGATGAAACCATTCAACACACAGAAGTTTTTTGTTACGCCAATCA
GGATATGGATGACAAAATTGAAGAGACTGATGCTCTGCAGAAAAATCCTTCCTCACTGACATCTAGTACTCTCACTAAAC
CTCTGGATTCTGCATGCTTGTCTGAAGAAACACACTCATATGTCACTAGCTACGAAATGCCCGCCAAAGACATTCCAAAA
AATGATGGAGAGATTTCACTAGAAGTAAGTGGTGTAGAGGGCACCTTGGCAGAAGAAAAATATTGTGGAGATGAAACTTG
TAGACACACAGTTTCAGGTGGAGATACAGACGAAAACAAACCTATAGAGGAAGACAACACTGATCAACTAAAGAGAAATA
GGATTACTTACTCTCAAATAGTTAAAGAAAGCAGGAGGTTTAATATTGATTTGGTATCAAAGCTCCTGTATTCTCAAGGG
TTGCTGATTGATCTTTTAATCAAATCAAATGTTAGTCGTTATGCAGAATTTAAAAATGTCACTAGGATTCTTGCATTTCG
AGAAGGAAAAGTAGAGCAGGTGCCTTGTTCCAGAGCAGATGTCTTCAATAGCAAAGAACTCACTATGGTTGAAAAGAGGA
TACTAATGAAATTTCTTACATTTTGTTTAGACTATGAACAACATCCTGACCAATACCAAGCTTTCATGCAATGCTCATTT
TCAGAGTACTTAAAAACTAAAAAATTAACCCCCAACCTCCAGCATTTTGTACTGCACTCCATTGCAATGACAGAATCATC
TTGCACTACAATAGATGGCCTTAAAGCAACAAAAAACTTCCTTCAGTGTCTTGGACGGTTTGGCAACACTCCCTTTTTAT
TTCCCTTATATGGCCAAGGAGAAATTCCCCAGTGTTTCTGCAGGATGTGTGCAGTTTTTGGTGGAATCTATTGTCTTCGC
CATAAAGTTCAATGCCTTGTAGTTGACAAAGAATCTGGAAGATGTAAAGCAATTATAGATCACTTAGGTCAAAGAATAAA
TGCTAAATATTTTATAGTGGAGGATAGTTACCTTTCTGAGAAAACATGCTCAAATATACAGTATAAGCAGATCTCCAGGG
CAGTGCTCATTACAGATCAATCTATACTGAAGACAGATTCAGATCAGCAAATTTCCATTTTGATAGTGCCTCCAGCGGAC
TCAGGAACGTGTGCCGTTCGTGTCACTGAATTATGTTCTTCAACCATGACGTGCATGAAAGACACTTATCTGGTACATCT
GACCTGTTCCTCCTCTAAAACAGCAAGAGAAGACTTAGAGTCAGTAGTAAAGAAACTATTCACTCCGTATACTGAAGCAG
CAATAAATGAGGAGGAACTTACAAAGCCAAGACTCTTGTGGGCTCTTTATTTTAATATGAGAGATTCCTCCGGAGTCAGC
AGAAGCTCATATAATGGCTTACCGTCCAATGTTTATGTCTGCTCTGGGCCCGACTGTGGACTGGGAAATGAGCATGCGGT
CAAGCAAGCTGAAACACTGTTCCGGGAGATCTTTCCAAGTGAAGAATTCTGTCCCCCACCTCCAAATCCAGAAGACATTA
TCTTTGATGGTGATGATAAACAACCAGAGGTCTCTGGAACCAATAACATAATCATGGCCAAACTAGACTCCTCTGAGGGA
AGCAAAAACCTAGAAAGCCCG
ORF - retro_fcat_1744 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.65 % |
| Parental protein coverage: | 99.23 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MADNLPSEFDVIVIGTGLPESITAAACSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENSDIVN |
| MAD.LP.EFDVI.IGTGLPESI.AAACSRSGQRVLH.DSRSYYGGNWASF.FSGLLSWLKEYQ..SD... | |
| Retrocopy | MADSLPTEFDVIIIGTGLPESILAAACSRSGQRVLHLDSRSYYGGNWASFNFSGLLSWLKEYQQKSDVAE |
| Parental | ENPA-WQEHILENEEAIALSRKDKTIQHVEVFCYASQDLHEDVEETGALQKNHASVTSVNPTEGEHSAYL |
| E..A.WQ..I.E.EEAI.L...D.TIQH.EVFCYA.QD.....EET.ALQKN..S.TS...T....SA.L | |
| Retrocopy | ESTASWQGLIHETEEAITLRKTDETIQHTEVFCYANQDMDDKIEETDALQKNPSSLTSSTLTKPLDSACL |
| Parental | PSEDESSSTVSCQMPTEQTPNSDLESSLEINDVEATGEEEKRCDDKTCVKSASEEETSENVLTTEDTTLQ |
| .SE...S...S..MP....P..D.E.SLE...VE.T..EEK.C.D.TC....S...T.EN....ED.T.Q | |
| Retrocopy | -SEETHSYVTSYEMPAKDIPKNDGEISLEVSGVEGTLAEEKYCGDETCRHTVSGGDTDENKPIEEDNTDQ |
| Parental | PRKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGRVEQVPCSRA |
| ...NRITYSQI.KE.RRFNIDLVSKLLYS.GLLIDLLIKSNVSRYAEFKN.TRILAFREG.VEQVPCSRA | |
| Retrocopy | LKRNRITYSQIVKESRRFNIDLVSKLLYSQGLLIDLLIKSNVSRYAEFKNVTRILAFREGKVEQVPCSRA |
| Parental | DVFNSKQLTMVEKRMLMKFLTFCMEYEKHPDEYKAYEEITFSEYLKTQKLTPNLQYFLLHSIAMTSETAS |
| DVFNSK.LTMVEKR.LMKFLTFC..YE.HPD.Y.A.....FSEYLKT.KLTPNLQ.F.LHSIAMT.E... | |
| Retrocopy | DVFNSKELTMVEKRILMKFLTFCLDYEQHPDQYQAFMQCSFSEYLKTKKLTPNLQHFVLHSIAMT-ESSC |
| Parental | NTIDGLKAAKNFLHCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAV |
| .TIDGLKA.KNFL.CLGR.GNTPFLFPLYGQGE.PQCFCRMCAVFGGIYCLRH.VQCLVVDKES..CKA. | |
| Retrocopy | TTIDGLKATKNFLQCLGRFGNTPFLFPLYGQGEIPQCFCRMCAVFGGIYCLRHKVQCLVVDKESGRCKAI |
| Parental | IDQFGQRIISKHFLVEDSYFSENTCSHVQYRQISRSVLITDRSVLKADSDQQISILTVPAVETGTFAVRV |
| ID..GQRI..K.F.VEDSY.SE.TCS..QY.QISR.VLITD.S.LK.DSDQQISIL.VP....GT.AVRV | |
| Retrocopy | IDHLGQRINAKYFIVEDSYLSEKTCSNIQYKQISRAVLITDQSILKTDSDQQISILIVPPADSGTCAVRV |
| Parental | IELCSSTMTCMKGTYLVHLTCTSSKTAREDLEPVVQKLFTPYTETEIENEEDEKPRLLWALYFNMRDSSD |
| .ELCSSTMTCMK.TYLVHLTC.SSKTAREDLE.VV.KLFTPYTE..I..EE..KPRLLWALYFNMRDSS. | |
| Retrocopy | TELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVVKKLFTPYTEAAINEEELTKPRLLWALYFNMRDSSG |
| Parental | VSRNSYNDLPSNIYVCSGPDCGLGNDNAVKQAETLFQQICPNEDFCPPPPNPEDIVIDGDSLQSEASESS |
| VSR.SYN.LPSN.YVCSGPDCGLGN..AVKQAETLF..I.P.E.FCPPPPNPEDI..DGD..Q.E.S... | |
| Retrocopy | VSRSSYNGLPSNVYVCSGPDCGLGNEHAVKQAETLFREIFPSEEFCPPPPNPEDIIFDGDDKQPEVSGTN |
| Parental | FIPEANSETPKESRSLGNP |
| .I..A.......S..L..P | |
| Retrocopy | NIIMAKLDSSEGSKNLESP |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP017611_brain | 48 .55 RPM | 29 .04 RPM |
| SRP017611_kidney | 5 .77 RPM | 13 .09 RPM |
| SRP017611_liver | 6 .07 RPM | 8 .79 RPM |
Felis catus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_fcat_1744 retrocopy.
Felis catus was not studied using FANTOM5 data.
retro_fcat_1744 was not experimentally validated.