RetrogeneDB ID: | retro_cfam_354 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 10:32862460..32863620(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCAFG00000001943 | ||
| Aliases: | CBWD2, CBWD1 | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cfam_354
GTCAGAGCTGTGGATGAGGAAGAGGAGCAGACAGAGGAGGACTGTCCTGAATTGATCCCCATTGAGATGAGGGAAGGAGA
GGAGGAGGAAAAGTCTGGTCCTGGTACCAAGATCCTAGTCACAATTATCACTAGGTATTAAGGGGCTAGGTGCACCAATA
CTTCTGAAAAATATCTTGATGGAGCAACATAAGAAAAGAGTAGTAGTTATTTCAAACAAATTTGGGGGAGAAAGTACAGT
GGAGAAATCCTTATCTGTCAGCCAAAGTGAAGTTCTCTACCAAAAATAGTTGGAACTTAGAAATGATTGCCTCTGCTATT
CTACTGAATAGGATAGTGGCCCTGGAGCTAACGAGAATGTGATGCAGAAGAAGGGAAAATTTGATGACATACCATTAAAG
ACCACTGGATTAGCAGATGCTGGTGCTGTAGCATCTTTGTTTTGGGGTTGATGCTGAATTAGGGATTAATATTTCTCTTA
TTAGTATCAGAACTCTTGTGGATACAAAATATGGATTAAAACATTTAGCAGTAGAAAAACTCGATGGTCTTATCCAGGAG
GCTTCTAGGCAAACTGCTTCAGCAGATACCATTATCATTAATAAAACAGATTGGGTTTCACAAGAGGATTTAAACAAATT
AAGAATCACCATTAGATCAATAAATGGACTGGGAAAATTTTTAGAAACACAAGGATCAAGAGCTGATCTCTCTAATATAC
TAGCTCTTCATGTCTTTGACAGTCTCTCTGGAATATATTTGCAGAAAAACTTCAACACTTACCAACCACACAGCCTTGCG
CTGATCAGAGCATCATCAACATCACATTTTAGAACCAAGCGATGTGAAGGAAGAAAGTCTAAATGGATTTATTCAGAATC
TTCTGTGGGTGAAGAATGTGAGAAGCAAGGACAATGACTGCATGCAGGTCAAGCAACTCAAGGGGCAGGTGTTGATCAAA
GACAAACCAAAACCAATGATTGTCCAAGGTGCCCATGAGCTCTATGATCTGGAGGAGAGCTGGAAAGAAGATACTGAGAG
AACGAATCAATTGGCTCTTATTGATGGGAATCTAGATGAGGACATCTTCAATAACTACTTATAGCTACTAAGACTGAAAC
AGAAAAGTGGTGGACAACACATTTCAAAGAAGATCAAGTT
ORF - retro_cfam_354 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.62 % |
| Parental protein coverage: | 98.48 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | VGAVDEEEEPAEEDCPELVPIETKLREEEEKSGPGAKIPVTIITGYLGA-GKTTLLNYILTEQHSKRVAV |
| V.AVDEEEE..EEDCPEL.PIE....EEEEKSGPG.KI.VTIIT.Y.GA.G...LL..IL.EQH.KRV.V | |
| Retrocopy | VRAVDEEEEQTEEDCPELIPIEMREGEEEEKSGPGTKILVTIITRY*GA>GAPILLKNILMEQHKKRVVV |
| Parental | ILNEFGEGSAVEKSLAVSQGGELYEEWLELRNGCLCCSVK-DNGLRAIENLMQKKGKFDYILLETTGLAD |
| I.N.FG..S.VEKSL.VSQ...LY...LELRN.CLC.S...D.G..A.EN.MQKKGKFD.I.L.TTGLAD | |
| Retrocopy | ISNKFGGESTVEKSLSVSQSEVLYQK*LELRNDCLCYSTE*DSGPGANENVMQKKGKFDDIPLKTTGLAD |
| Parental | PGAVASMFW-VDAELGVDIYLDGIITVVDSKYGLKHLEEEKPDGLINEASRQVALADIIIINKTDLVSEE |
| .GAVAS.FW.VDAELG..I.L..I.T.VD.KYGLKHL..EK.DGLI.EASRQ.A.AD.IIINKTD.VS.E | |
| Retrocopy | AGAVASLFW>VDAELGINISLISIRTLVDTKYGLKHLAVEKLDGLIQEASRQTASADTIIINKTDWVSQE |
| Parental | DLSKLRAAIRSINGLGKILETQRSRVDLSNVLDLHAFDSLSGISLQK-KLQHVPTTQPHLDQSIITVTF- |
| DL.KLR..IRSINGLGK.LETQ.SR.DLSN.L.LH.FDSLSGI.LQK.KLQH.PTTQP..DQSII..TF. | |
| Retrocopy | DLNKLRITIRSINGLGKFLETQGSRADLSNILALHVFDSLSGIYLQK<KLQHLPTTQPCADQSIINITF< |
| Parental | EVPGNAKEESLNVFIQNLLWEKNIRNKDDDCMEVIRLKGLVSIKDKAKQVIVQGVHELYDLEETPLSWKD |
| ..P...KEESLN.FIQNLLW.KN.R.KD.DCM.V..LKG.V.IKDK.K..IVQG.HELYDLEE...SWK. | |
| Retrocopy | LEPSDVKEESLNGFIQNLLWVKNVRSKDNDCMQVKQLKGQVLIKDKPKPMIVQGAHELYDLEE---SWKE |
| Parental | DTERTNRLVLIGRNLDKEI-LRQLFVATVTEAEKRWTTHFKEDQV |
| DTERTN.L.LI..NLD..I.L..L..AT.TE.EK.WTTHFKEDQV | |
| Retrocopy | DTERTNQLALIDGNLDEDI<LQ*LLIATKTETEKWWTTHFKEDQV |
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 | 0 .00 RPM | 40 .95 RPM |
| SRP017611_brain | 0 .00 RPM | 21 .20 RPM |
| SRP017611_kidney | 0 .00 RPM | 44 .58 RPM |
| SRP017611_liver | 0 .00 RPM | 7 .25 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_354 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_354 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_354 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000001943 | 1 retrocopy |
retro_cfam_354 ,
|
| Sarcophilus harrisii | ENSSHAG00000001103 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000001371 | 1 retrocopy |