RetrogeneDB ID: | retro_ggal_12 | ||
Retrocopy location | Organism: | Chicken (Gallus gallus) | |
| Coordinates: | 1:154833003..154833727(+) | ||
| Located in intron of: | ENSGALG00000016926 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRAIP | ||
| Ensembl ID: | ENSGALG00000002908 | ||
| Aliases: | None | ||
| Description: | TRAF-interacting protein [Source:RefSeq peptide;Acc:NP_001025757] |
Retrocopy-Parental alignment summary:
>retro_ggal_12
TTCCAATGGTTCAATATGGTGACTGCCTGCACCTACCCTCAGTGCAGGATCCAGATCAGCAAAAGATAGGTTATCAGTAA
ACTCTTCTTTGATGTTGCCCTGGAAGAGCAGACTGAACTGGATGCAGAAACCTTACAGAATGAAAAGGACAGGGTGAAGG
CTCAGCTCTCTGTGAAAGAGAAGAAAAAATGGGAGTGCCGGGCCATTGTGGATGCGCTGTGGGATGCTCTGGACACGTGT
GGTGCCATAACAGAGTTGCTCTAGAAGCTACTGGGAGAGACAGAGAGATGCTGTTCCTCCCTCAAGAAACAGGTGAAATT
CCTGGAGAAGCAGCAGGAGGATAACAGATGATCAGAAGAAGACCCACCACCAGCAAAACAAGCTGGGAACCATGGAGTGG
ATTGAATTGTTGCTTCCGAGCTAGTGCAGTGAAGTGGGGGAGATGATGAGAGAGATGGGAGTTGGGCAGGCAGCAGTAAA
GCAGCTTGCTATCTACTGTGTCTCACTGAGGGAGGAATATGTGAACTTGAAGGAGACTTGGAAGATGTCTGGTGAGATGA
CAGAGAACAGAAGGAGTTATTCTCTGTCAACAATAAGCTGCAGAAAACAGTTTCAGAGTTGGATAAGATAAAGGAGGAGT
TAAAAAGCACCCAGAAGGATCTGAAAAATGCAGACAAGGGAGATCCTGAGTTTGAGGGAGACATCTATAATCAGAGAGAC
AACC
ORF - retro_ggal_12 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.89 % |
| Parental protein coverage: | 52.37 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | FQWFDTAPSRTCPQCRIQVSKRHIISKLFFDVALEEQTALDAETLQNELDKVKAQLSMKEKEKRECQAIV |
| FQWF......T.PQCRIQ.SKR..ISKLFFDVALEEQT.LDAETLQNE.D.VKAQLS.KEK.K.EC.AIV | |
| Retrocopy | FQWFNMVTACTYPQCRIQISKR*VISKLFFDVALEEQTELDAETLQNEKDRVKAQLSVKEKKKWECRAIV |
| Parental | DGLRDTLDVRNATIESLQKVLGETEMLCSSLKKQMKFLEQQQEDNRSSKEE-ARRLRNKLKTMERIELLL |
| D.L.D.LD...A..E.L.K.LGETE..CSSLKKQ.KFLE..Q.......EE......NKL.TME.IELLL | |
| Retrocopy | DALWDALDTCGAITELL*KLLGETERCCSSLKKQVKFLEK-QQEDNR*SEE>THHQQNKLGTMEWIELLL |
| Parental | QSQRPEVEEMIREMGVGQAAVEQLAVYCVSLKKEYENLKEARKISSEMTE-KQKKELFFVNSKLQKTVSE |
| .S...EV.EM.REMGVGQAAV.QLA.YCVSL..EY.NLKE..K.S.EMTE..QK.ELF.VN.KLQKTVSE | |
| Retrocopy | PS*CSEVGEMMREMGVGQAAVKQLAIYCVSLREEYVNLKETWKMSGEMTE<EQK-ELFSVNNKLQKTVSE |
| Parental | LEKTKEELKSTQKDLKNADK-EILSLKKKIDILQDT |
| L.K.KEELKSTQKDLKNADK.EILSL.....I...T | |
| Retrocopy | LDKIKEELKSTQKDLKNADK>EILSLRETSIIRETT |
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 |
|---|---|---|
| SRP007412_brain | 0 .06 RPM | 8 .25 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 0 .22 RPM |
| SRP007412_heart | 0 .05 RPM | 0 .35 RPM |
| SRP007412_kidney | 0 .06 RPM | 0 .50 RPM |
| SRP007412_liver | 0 .19 RPM | 0 .15 RPM |
| SRP007412_testis | 0 .21 RPM | 21 .49 RPM |
Gallus gallus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ggal_12 retrocopy.
Gallus gallus was not studied using FANTOM5 data.
retro_ggal_12 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ggal_12 has 0 orthologous retrocopies within neognath group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Gallus gallus | ENSGALG00000002908 | 1 retrocopy |
retro_ggal_12 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000013769 | 1 retrocopy |