RetrogeneDB ID: | retro_btau_234 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | X:129541463..129542201(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000013625 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CD63 | ||
| Ensembl ID: | ENSBTAG00000011931 | ||
| Aliases: | None | ||
| Description: | CD63 antigen [Source:UniProtKB/Swiss-Prot;Acc:Q9XSK2] |
Retrocopy-Parental alignment summary:
>retro_btau_234
TGCACAGCCTTCTGGAGCCCAAGCCTGGCAGCCATGGTGGTGGAAGGAGGAATGAAATGTGTCAAGGCCTTGCTCTATGT
TCTTCTGCTGACCTGTTGCATCTGTGCAGTGGGACTGATTGCTGTGGGCTTAGGGGCCAAGCTCGACCTGAATCAGACCA
CTAACTGGGAGGCCACCCCTGAATCCCTGGTGCCCGTGGTCATCATCGCAATGAGTATATGCCTCTTCCTAGTGGCCTTT
GTGGGCTGCTATGGGGCCTGGAAGGAAGACTACTGTCTTATGATCATGCTTGCCATCTGCTTGTCCCTAATCATGCTGGC
GGAGGTGGCTGCAGTCGTTGCTGGCTATATGCTTGAAGATAAGGTGATGTCAGAATCTAATAAGGACTTCCAGCAGCAGA
TACAGAATTATCAAAAAAACAATCACATGTCACCGATTATGGACAGGATGCAGGAACATTTTAAGTGCTGCAGGGCAGCT
AACTACACAGACTGGGAATACATCCTGCTCACGACCAAGCGAGTCCCTGGCTCCTACTGTGTCAGCATCACTAAAGGCTG
TGGGATTAATTTCAGCATAAAGGAGATGCATGCTGAAAGCTGTGTGGCGAAGACGGGGGGCTGGCTGAGGAGCAAAGTGG
TGATTGCAACGGGCTTGAGCATTGCCTTTATGGAGGTCCTGGTTATTGTCTTTGCCTGCTGCCTTGTGAAGGGCATCCGA
CATGGCTATGATGATGTC
ORF - retro_btau_234 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.83 % |
| Parental protein coverage: | 99.16 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAVEGGMKCVKFLLYVLLLVFCACAVGLIAVGVGTHLVLNQTITHGATPSFLLPVVIIAVGAFLFLVAFV |
| M.VEGGMKCVK.LLYVLLL..C.CAVGLIAVG.G..L.LNQT....ATP..L.PVVIIA....LFLVAFV | |
| Retrocopy | MVVEGGMKCVKALLYVLLLTCCICAVGLIAVGLGAKLDLNQTTNWEATPESLVPVVIIAMSICLFLVAFV |
| Parental | GCCGACKENYCLMITFAIFLSLIMLVEVAAAIAGYVFRDKVRSEFNKDFRQQMKNYPKDNQTASILDKMQ |
| GC.GA.KE.YCLMI..AI.LSLIML.EVAA..AGY...DKV.SE.NKDF.QQ..NY.K.N....I.D.MQ | |
| Retrocopy | GCYGAWKEDYCLMIMLAICLSLIMLAEVAAVVAGYMLEDKVMSESNKDFQQQIQNYQKNNHMSPIMDRMQ |
| Parental | KDFECCGAANYTDWEKILAVTNKVPDSCCVNITHNCGINFVVKDIHTEGCVEKIAAWLRKNVLVVAAAAL |
| ..F.CC.AANYTDWE.IL..T..VP.S.CV.IT..CGINF..K..H.E.CV.K...WLR..V....A..L | |
| Retrocopy | EHFKCCRAANYTDWEYILLTTKRVPGSYCVSITKGCGINFSIKEMHAESCVAKTGGWLRSKVVI--ATGL |
| Parental | GIAFVEILGIVLACCLVKSIRSGYE |
| .IAF.E.L.IV.ACCLVK.IR.GY. | |
| Retrocopy | SIAFMEVLVIVFACCLVKGIRHGYD |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 108 .43 RPM |
| ERP005899_muscle | 0 .00 RPM | 327 .50 RPM |
| SRP017611_brain | 0 .00 RPM | 59 .15 RPM |
| SRP017611_kidney | 0 .00 RPM | 274 .07 RPM |
| SRP017611_liver | 0 .00 RPM | 197 .68 RPM |
| SRP030211_testis | 4 .51 RPM | 74 .57 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_234 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_234 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_234 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000002415 | 2 retrocopies | |
| Bos taurus | ENSBTAG00000011931 | 1 retrocopy |
retro_btau_234 ,
|
| Callithrix jacchus | ENSCJAG00000007935 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000009142 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000025351 | 1 retrocopy |