RetrogeneDB ID: | retro_cfam_218 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 1:106657540..106659124(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000003428 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NUP62CL | ||
| Ensembl ID: | ENSCAFG00000017963 | ||
| Aliases: | None | ||
| Description: | nucleoporin 62kDa C-terminal like [Source:HGNC Symbol;Acc:25960] |
Retrocopy-Parental alignment summary:
>retro_cfam_218
ATGAGTGGGTTTAATTTTGGAGGCACTGGGGCCCCCACAGGTGGGTTCACATTTGGCACTGCAAAGACGGCGACAACCAC
TCCTGCTACTGGGTTTTCTTTCTCTACATCTGGCACTGGTGGGTTTAATTTTGGGACTCCCTCCCAGCCAGCTGCAAGTA
CTCCTTCTACTGGCCTCTTCTCCCTCACAACCCAGGCTCCAGCAACACAAACCCCAGGATTCAGTTTTGGAACCACAACT
CCTGCCACAGGAGGAACTGGATTCTCCTTAGGCATCAGCACACCAAAGCTAAACTTGGGCAGCGTGGCTGCCACCCCAGC
TACAGCACACCCTGGCGGCTTTGGGCTCAGCAGCAGCACCCTCACCAATGCCATCTCGAGCACTGTCACCTCCAGCCAGA
GCACAGCACCCACCGGCTTCATGTTTGGCTCTGCCACCACCTCTGCTGCTCCTTCCACCACACCAGGGGGATTCTCATTC
ACAGCGGGGAGCACGTCCCAGACCGGGACCTCAGGTTTTAATATTGGCTCAATGGGGACTTCAACCCAGCCCACGGCACT
TGCTGGATTGCTCTTCACTCCTGCCACTCCAGCAGCCACTGGAGCGGGAGCCACACAGCCAGCTGCTCCTGCACCCACTG
CTGCCACTACCAGTGCTGGGCCCACACTGTTTGCCTCTCTAGCAACTGCTCCAACCTCATCGACCACCACTGGGCTTTCT
CTTTGTACCCCATCAACCACGGCTGGAACTCCTGGAGCTGGAACACTGGGCTTCAGCTTAAAGGCCACTGGAGCAGCTTC
TACGGCCTCCACAACAACATCCACCACCACGGCCACCACCACCACTGCAGCCACCACTGCAGCCACCACTACCACCACTG
GCTTTGCCTTGAATCTGAAGCCCCTTGCACCGGCCGGGATCACCAGCAATGCACCGGCTGCTGTGGCCGCACCACCTGGC
CCTGGTGCAGCCACTGGGGCATCTACCAGCCCTGTGATGACCTACGCCCAGCTGGAGAGTCTGATCAACAAGTGGAGTCT
GGAGCTGGAGGACCAGGAACGGCACTTCCTGCAGCAGGCCACACAGGTCAATGCCTGGGACCGCACACTGATTGAGAATG
GGGAGAAGATCACTACCCTCCACCGTGAGGTGGAGAAAGTGAAGCTGGACCAGAAGAGGCTGGACCAAGAGCTCGACTTC
ATCCTGTCTCAGCAGAAGGAGTTGGAAGACCTGCTGAGCCCACTGGAGGAGTCGGTCAAGGAGCAGAGTGGCACTGTCTA
CCTGCAGCATGCCGATGAGGAGCGTGAGAAAACCTACAAGCTGGCAGAGAATATCGATGCACAGCTAAAGCGCATGGCCC
AAGACCTCAAGGACATCATCGAGCACTTGAACACATCTGGAGGCCCTGCCGACACCAGCGACCCACTGCAGCAGATCTGC
AAGATCCTCAATGCGCACATGGACTCGCTGCAGTGGATCGACCAGAACTCGGCCCTGTTGCAGAGGAAGGTGGAGGAGGT
GACCAAGGTGTGTGAGGGGCGTCGCAAGGAGCAGGAGCGCAGCTTCCGGATCACATTCGACTGA
ORF - retro_cfam_218 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.51 % |
| Parental protein coverage: | 99.81 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ISGFNFGETGTPSGGFTFGPAKTVTTTSAIGFTFSTPGARGFKFRTLPQPV-STSSTALFSFSNAAPASQ |
| .SGFNFG.TG.P.GGFTFG.AKT.TTT.A.GF.FST.G..GF.F.T..QP..ST.ST.LFS....APA.Q | |
| Retrocopy | MSGFNFGGTGAPTGGFTFGTAKTATTTPATGFSFSTSGTGGFNFGTPSQPAASTPSTGLFSLTTQAPATQ |
| Parental | TKPFSFGIP-PATEETGFSLRISAPKLNLGNTCSLIQPAVITGASRLSTSTLTNTLTCSVPSYWVTA-SS |
| T..FSFG...PAT..TGFSL.IS.PKLNLG........A...G...LS.STLTN.....V.S...TA... | |
| Retrocopy | TPGFSFGTTTPATGGTGFSLGISTPKLNLGSVAATPATAH-PGGFGLSSSTLTNAISSTVTSSQSTAPTG |
| Parental | FVFGSAITSATESATATGFSFISGSIASNPNMTHFSCWSLIEKAWPTSITPTPSTPSIQLTTVIPSTCLA |
| F.FGSA.TSA..S.T..GFSF..GS..S......F...S......PT.......TP.....T....T..A | |
| Retrocopy | FMFGSATTSAAPSTTPGGFSFTAGS-TSQTGTSGFNIGSMGTSTQPTALAGLLFTPATPAATGAGATQPA |
| Parental | SASAADATTCSGTMLFTSTSNASTSAAATGLSFGAPATSMGTFGGITLGFGLKFPGAGGAAHTASTTAST |
| ......ATT..G..LF.S...A.TS...TGLS...P.T..GT.G..TLGF.LK...A.GAA.TASTT.ST | |
| Retrocopy | APAPTAATTSAGPTLFASLATAPTSSTTTGLSLCTPSTTAGTPGAGTLGFSLK---ATGAASTASTTTST |
| Parental | TTTTTVTTTTT--TTTTSGFTLNLRSLTSAGINNIVPVGINSLPFT-STVNAIVTPVMTYGQLEGLINKW |
| TT.TT.T..TT..TTTT.GF.LNL..L..AGI....P......P.......A...PVMTY.QLE.LINKW | |
| Retrocopy | TTATTTTAATTAATTTTTGFALNLKPLAPAGITSNAPAAVAAPPGPGAATGASTSPVMTYAQLESLINKW |
| Parental | SLDLEDQEKYFLHQATQVNAWDRTLIENGEKITTLHGEVEKVKLDQQRLEQELDFILSQQKELEDLLTPL |
| SL.LEDQE..FL.QATQVNAWDRTLIENGEKITTLH.EVEKVKLDQ.RL.QELDFILSQQKELEDLL.PL | |
| Retrocopy | SLELEDQERHFLQQATQVNAWDRTLIENGEKITTLHREVEKVKLDQKRLDQELDFILSQQKELEDLLSPL |
| Parental | EEFVKDQSGSVYLQHADKVHGKTYRLAENIDAQLKRMAQDLKDIIEHLNTFGSPADTTDPLQQICKILNA |
| EE.VK.QSG.VYLQHAD....KTY.LAENIDAQLKRMAQDLKDIIEHLNT.G.PADT.DPLQQICKILNA | |
| Retrocopy | EESVKEQSGTVYLQHADEEREKTYKLAENIDAQLKRMAQDLKDIIEHLNTSGGPADTSDPLQQICKILNA |
| Parental | HMDSLQWINQNSVRLKPKIMERKTNAKKQLKKFQQSIYIKF |
| HMDSLQWI.QNS..L..K..E.........K....S..I.F | |
| Retrocopy | HMDSLQWIDQNSALLQRKVEEVTKVCEGRRKEQERSFRITF |
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 |
|---|---|---|
| SRP012049_cerebellum | 29 .99 RPM | 2 .73 RPM |
| SRP017611_brain | 19 .85 RPM | 0 .32 RPM |
| SRP017611_kidney | 15 .72 RPM | 0 .92 RPM |
| SRP017611_liver | 13 .34 RPM | 0 .00 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_218 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_218 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_218 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000017963 | 1 retrocopy |
retro_cfam_218 ,
|
| Dasypus novemcinctus | ENSDNOG00000001467 | 1 retrocopy | |
| Felis catus | ENSFCAG00000001984 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000001005 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000013865 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000001787 | 1 retrocopy | |
| Vicugna pacos | ENSVPAG00000003649 | 1 retrocopy |