RetrogeneDB ID: | retro_btau_1666 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 9:7645891..7646729(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PRKAR1A | ||
| Ensembl ID: | ENSBTAG00000008621 | ||
| Aliases: | None | ||
| Description: | cAMP-dependent protein kinase type I-alpha regulatory subunit [Source:UniProtKB/Swiss-Prot;Acc:P00514] |
Retrocopy-Parental alignment summary:
>retro_btau_1666
CTGGCTCCTGGTGGCACCTCTGCTGAGGAGGAGCGCAGCTCCTGGGAACGTGAACTCTACGACCAGAAGCACACATCTAG
GCCCTGTTCAAAGAGTCCATCATGTAGCTGTGCACTGCACGGCCCGAGAGGCCATGACATTCCTCAGGGAATACTTTGAG
AGGTTGGAGAAGAAGGAGGCAAAACGGATCCAGAATCTGCAGAAAGCAAGCTCTTGTGCAGACTGAAGGAAGGATGAAGT
CTCTCTCCCTCCAACCAACCCAGCGATGAGGGGCTGGGGGCAACAAGGTGCCATCTACGCTGAGGTCTACACTAAGCAAG
ATGCCACATCCTATGTTAGGAAGGTTGGACCAGAAGGTTACAAGACAATGACTGCTTTAGCTAAAGCTGTTGAAAAGAAT
GTGCTCTCTGCACATCTTGATGATAGTGAGAGAAGCAATCATTTTGATGCCGTGTTTCCAGTTTCCTTTATTGCTGGAGA
GATTGTCATTCAGCAAGGTCGTGAAAGGAATAACTTCTTTGTGATTGATCAAGGAGAAATGGAAGTCTGTGTCAACAGTG
AATGGGCAACCAGTGTCGGGGAAGGAAGGAGTGTTGGGGAAATTGCTTCGATCATGGAGCACCTAGAGCAGCTACCTTCA
AGGCCCAGACAGATGTGAAGTTGTGGGGCATCGCCCCAAGACAACTCTAGAAGGATCCTATCGGGAAGTGTGCGAAGAAA
GCTGAAGATGTATGAGGAGTCTTTTAGCAAGGGATCTATTTTAGCATTTCTGGACAAGTGGAAACATCTCAGGGTAGCTG
ATGCCATGGAACTGGTCCAGACTGAAGACAGCCAGAAG
ORF - retro_btau_1666 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.66 % |
| Parental protein coverage: | 73.68 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MASGTTASEEERSLRECELYVQKH-NIQALLKDSIVQLCTARPERP-MAFLREYFEKLEKEEAKQIQNLQ |
| .A.G.T..EEERS..E.ELY.QKH..I.AL.K.SI..LCTARPERP.M.FLREYFE.LEK.EAK.IQNLQ | |
| Retrocopy | LAPGGTSAEEERSSWERELYDQKH<HI*ALFKESIM*LCTARPERP<MTFLREYFERLEKKEAKRIQNLQ |
| Parental | KAGSRADSREDEISPPPPNPVVKGRRRRGAISAEVYTEEDAASYVRKVIPKDYKTMAALAKAIEKNVLFS |
| KA.S.AD.R.DE.S.PP.NP...G....GAI.AEVYT..DA.SYVRKV.P..YKTM.ALAKA.EKNVL.. | |
| Retrocopy | KASSCAD*RKDEVSLPPTNPAMRGWGQQGAIYAEVYTKQDATSYVRKVGPEGYKTMTALAKAVEKNVLSA |
| Parental | HLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMDVYVNNEWATSVGEGGSFGELALI-YG |
| HLDD.ERS..FDA.FPVSFIAGE.VIQQG.E..NF.VIDQGEM.V.VN.EWATSVGEG.S.GE.A.I..G | |
| Retrocopy | HLDDSERSNHFDAVFPVSFIAGEIVIQQGRERNNFFVIDQGEMEVCVNSEWATSVGEGRSVGEIASI<HG |
| Parental | TPRAATVKAKTNVKLWGI-DRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFE |
| .PRAAT.KA.T.VKLWGI...D..RRIL.GS..RK.KMYEE..SK.SIL..LDKW..L.VADA.E.VQ.E | |
| Retrocopy | APRAATFKAQTDVKLWGI>PQDNSRRILSGSVRRKLKMYEESFSKGSILAFLDKWKHLRVADAMELVQTE |
| Parental | DGQK |
| D.QK | |
| Retrocopy | DSQK |
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 | 28 .05 RPM |
| ERP005899_muscle | 0 .05 RPM | 90 .69 RPM |
| SRP017611_brain | 0 .05 RPM | 148 .59 RPM |
| SRP017611_kidney | 0 .00 RPM | 156 .48 RPM |
| SRP017611_liver | 0 .00 RPM | 47 .80 RPM |
| SRP030211_testis | 0 .04 RPM | 241 .80 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1666 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1666 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1666 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000008621 | 1 retrocopy |
retro_btau_1666 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000012903 | 1 retrocopy |