RetrogeneDB ID: | retro_btau_1748 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | X:72584543..72585195(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM168A | ||
| Ensembl ID: | ENSBTAG00000016497 | ||
| Aliases: | None | ||
| Description: | protein FAM168A [Source:RefSeq peptide;Acc:NP_001192501] |
Retrocopy-Parental alignment summary:
>retro_btau_1748
GCTTATACAAGTTATCCCACAGCCTATCCAATTGCAGCCCCTGCTTACAATCCCAGCCTGTACCCTGCCACTAGCTCCCC
TTATGCTCCAGCAACTCTGCTGATGAAATAGACCTGGCTAGAGAACTCATCTTCCTGTGCCACTGAAGGTACCTATTTCT
ACCTCCCAGTGGACACCAGGACCGAGAGCCAAACTTACCAAACATCCTCTGCAGCTTTCAGATATACAGAGGGGACACCA
TACAAGGTCCCACCAGCCCAGAGTAATACTGCCCTGATCCCCCTACTCCTCTTCACCCAATCCCTATCAGATGGTCATGC
ATCCAATCATAAGTGCCTACCCCTAGCAGAATCTGTATGTCCTGGGAGCCTAGGACACAAAGCTGGTGTATGCTGCCCAG
GCTTATGTCATCCACTACACCATGGTCATCCAGCCTAACAGTACTCACTCTGCCATCTACCAGACACCAGTAAACCCTCC
CAATACCAATGTCATGGCCATGGGCATGGTGGCTGGCACCACCGTGATGATGTCAACATGTACCCTGCTGACTGCATCAC
AGCACACAGCGATTGGGGCATACCCTGTCTTCATGCCAACATACAGGGCACAAGGGATCCTTGCATACAGCTATATATAT
GCCCCACACTGG
ORF - retro_btau_1748 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.57 % |
| Parental protein coverage: | 97.35 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AYPAAAPAYNPSLYPTNSPSYAPEFQFLHSAYATLLMKQAWPQNSSSCGTEGT-FHLPVDTGTENRTYQA |
| AY.....AY.P...P...PS..P.......A.ATLLMK..W..NSSSC.TEGT.F.LPVDT.TE..TYQ. | |
| Retrocopy | AYTSYPTAY-PIAAPAYNPSLYPATSSPY-APATLLMK*TWLENSSSCATEGTYFYLPVDTRTESQTYQT |
| Parental | SSAAFRYTAGTPYKVPPTQSNTAP-PPYSPSPNPYQTAMYPIRSAYPQQNLYAQGAYYTQPVYAAQPHVI |
| SSAAFRYT.GTPYKVPP.QSNTA...PYS.SPNPYQ..M.PI.SAYP.QNLY..GA..T..VYAAQ..VI | |
| Retrocopy | SSAAFRYTEGTPYKVPPAQSNTAL>SPYSSSPNPYQMVMHPIISAYP*QNLYVLGA*DTKLVYAAQAYVI |
| Parental | HHTTVVQPNSIPSAIYPAPVAAPRTNGVAMGMVAGTTMAMSAGCSGTLLTAPQHTAIGAHPVSMPTYRAQ |
| H.T.V.QPNS..SAIY..PV..P.TN..AMGMVAGTT..MS.....TLLTA.QHTAIGA.PV.MPTYRAQ | |
| Retrocopy | HYTMVIQPNSTHSAIYQTPVNPPNTNVMAMGMVAGTTVMMS---TCTLLTASQHTAIGAYPVFMPTYRAQ |
| Parental | GTPAYSYV-PPHW |
| G..AYSY...PHW | |
| Retrocopy | GILAYSYIYAPHW |
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 | 0 .65 RPM |
| ERP005899_muscle | 0 .00 RPM | 4 .75 RPM |
| SRP017611_brain | 0 .00 RPM | 19 .19 RPM |
| SRP017611_kidney | 0 .00 RPM | 8 .42 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .72 RPM |
| SRP030211_testis | 0 .00 RPM | 2 .55 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1748 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1748 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1748 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 | ENSBTAG00000016497 | 1 retrocopy |
retro_btau_1748 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000014507 | 1 retrocopy |