RetrogeneDB ID: | retro_btau_270 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 1:93990771..93992476(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000046279 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZKSCAN2 | ||
| Ensembl ID: | ENSBTAG00000011162 | ||
| Aliases: | None | ||
| Description: | zinc finger protein with KRAB and SCAN domains 2 [Source:RefSeq peptide;Acc:NP_001192599] |
Retrocopy-Parental alignment summary:
>retro_btau_270
CCTTCGAATACCAGAACAGTGTCGGACCAAGTTCAAAAATCTGCGGAAGAGTTACCGAAAAGTGAGAAATGGCCATGTGC
CTTCTTTGAGGACATGGGCACTTTGTTGAATCCTGCAGCACATGTTTCATCCACAGATAAGCCAAGGGAGATCTGTCTCT
CCCCAAACTGAAGATAACTGGCATCAGTGCTGAAGCACAGATCAATTTGGTGGAGGAGGAAGAAGCTGCAGAGGAGTCTG
ATGGTGATGAAATGGGCGTTGAGTTTATCTGGAAGCCTGAGCTTCATGGTGGCCCTGTCATATTTCAAAACCTGAGTGGT
GTGCACGGGGGCTACGAGGAAACCAAGACTTTCCTTGACATCCTCCATGAGACTTGGTCTTATGAAGTGCTGCAAGCCTG
TCATCAGAAGAGCAAGTGGTATGGGACCGTGGCTGAGCAGCTTCGAGAGTGTGGCTTCCTCCAAACTCCGGAACAGTGCC
AGACCAAGTTCAAAAGCCTTCAGAAGAGTCACCTCAAAGTGAAAAATGGTCATGTGCTAGACTCCTGCAGATCCTACAAG
GAGATGGATGCCCTGATTAACTCTCGGGCATCTGCTTCTCCCACCATTTCCCCAGAAGAAGCCCCATCGTCCTCAGTTCA
AGAAAGAGACATCATGGAAATTGAACCTCAGGAATCTACAGGCTGGGAACCTGAGGAGGACTCCCAGGAGGCACTTGTTG
AAGATTCTGGCAGCGAGAGAATGAGTGAGGAGGAAATCATACAAGAACCAGAATTCCAGGGACCTCCAGGTTTACTGCAA
AACCCGAGTGATTTTGAAATTGAAAGTAGTATCAAAGAGGATACAACACAGGTAATCTGTAAGGACATGGAGCAGCATAC
GGCATTCGTAGAAAAGTCTAAAAGGGTCGTTTTCCAGAATGTTGATCCAGGTAAATATCATAAAAGGGATTACATCTCAG
GAAGACAGTGGGAAAACCTTCATGGAATTGGACAGGGAAAACTGGTGCATCAGCCTCGAGATTTGGGGAAAGCCATAGTG
CATCAGAGGCCTTTTGTGGGGAAGAGGCCCTTCCGGCTCCTCAGATATGGAGAAAGCTTTAGAAGGAGTGAGCGTCTCAT
GTGCCGCATGACCCACCAGAAGGAAAACCCTTCTAAGTGCAGTGTCTGTGGGAAGTGCTTCGGTAGAAGCAGGAGTCTAG
TCCAACACCAAAGAATCCACACTGGGGAAAAGCCTTTTAAATGTCTCAACTGCGGGAAAAGCTTTACGACTCCTCCAACT
TTGGTGCCCGCCAGAGAATTCATACAGGAGAGAAAAACTACACATGTGGAGAGTGTGGGAAATGCTGCAGCCAGAGCTCC
AGTCTCATTATACACCAGAGAACCCACACTGGACAGAAGCCCTACCAGTGTGGTGAGTGCGGGAGGAGCTTCACCAACAG
TTCGCACTTCAGTGCCCACCAGAGAGTCCACACTGGCAAGAATCCCTACAAGTGTGTGGACTGTGAGAAAAGTTTCAATA
ACTGTAGGAGATTTCGCGAGGACCGGCGAGTACACACCAGGGAGAAGCCCTACAGGTGCAGCCAGTGTGGCAGACATTTC
AGCAAGAGTTTTGTGCTCATTAAACTTCGGGAGGTTCACATCAGAGAAAAGCTGCTGCCACCCCTGCCAGTATTCTGCTC
CCCGGAGAACCCCCTCAAGGGGAAG
ORF - retro_btau_270 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.87 % |
| Parental protein coverage: | 58.82 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | PEQCRTKFKSLQKSYRKVRNGHVLEPCAFFEDMDALLNPSAHASSMDKPKEI-LSLPRLKRIGISAKEQI |
| P...RT.....QKS...........PCAFFEDM..LLNP.AH.SS.DKP.EI.LSLP.LK..GISA..QI | |
| Retrocopy | PSNTRTVSDQVQKSAEELPKSEKW-PCAFFEDMGTLLNPAAHVSSTDKPREI<LSLPKLKITGISAEAQI |
| Parental | NLVEEEEAAEESDGDEMGIEFIRKPELHGAPVIFQNLSGVHWGYEETKTFLDILHETRFYEALQACHRKS |
| NLVEEEEAAEESDGDEMG.EFI.KPELHG.PVIFQNLSGVH.GYEETKTFLDILHET..YE.LQACH.KS | |
| Retrocopy | NLVEEEEAAEESDGDEMGVEFIWKPELHGGPVIFQNLSGVHGGYEETKTFLDILHETWSYEVLQACHQKS |
| Parental | KLYGAVAEQLRECGFLRTPEQCRTKFKSLQKSYRKVKNGHVLESCAFYKEMDALINSRASAAPTSSPEEA |
| K.YG.VAEQLRECGFL.TPEQC.TKFKSLQKS..KVKNGHVL.SC..YKEMDALINSRASA.PT.SPEEA | |
| Retrocopy | KWYGTVAEQLRECGFLQTPEQCQTKFKSLQKSHLKVKNGHVLDSCRSYKEMDALINSRASASPTISPEEA |
| Parental | PSPSVQEREDMEIEPQEPTVWEPEEDSQEVLVEDSGSERMSEEEIMQEPEFQGPPCLLQSPSDFEIESSI |
| PS.SVQER..MEIEPQE.T.WEPEEDSQE.LVEDSGSERMSEEEI.QEPEFQGPP.LLQ.PSDFEIESSI | |
| Retrocopy | PSSSVQERDIMEIEPQESTGWEPEEDSQEALVEDSGSERMSEEEIIQEPEFQGPPGLLQNPSDFEIESSI |
| Parental | KEDATQVICKDMEQHRAFIEKSKRVVSQNVDPGKYCKRDCVSGGQWENLHGIRQGKLMPQPRDLGKAVVH |
| KED.TQVICKDMEQH.AF.EKSKRVV.QNVDPGKY.KRD..SG.QWENLHGI.QGKL..QPRDLGKA.VH | |
| Retrocopy | KEDTTQVICKDMEQHTAFVEKSKRVVFQNVDPGKYHKRDYISGRQWENLHGIGQGKLVHQPRDLGKAIVH |
| Parental | QRPLVGKRPFRLLRYGESFGRSARLMCRMTHQKENPSKCSVCGKCFGRSRSLVRHQRIHTGEKPFKCLDC |
| QRP.VGKRPFRLLRYGESF.RS.RLMCRMTHQKENPSKCSVCGKCFGRSRSLV.HQRIHTGEKPFKCL.C | |
| Retrocopy | QRPFVGKRPFRLLRYGESFRRSERLMCRMTHQKENPSKCSVCGKCFGRSRSLVQHQRIHTGEKPFKCLNC |
| Parental | GKSFN-DSSNFGAHQRIHTGEKPYRCGECGKCFSQSSSLIIHQRTHTGEKPYQCGDCGRSFTNSSHFSAH |
| GKSF..DSSNFGA.QRIHTGEK.Y.CGECGKC.SQSSSLIIHQRTHTG.KPYQCG.CGRSFTNSSHFSAH | |
| Retrocopy | GKSFT<DSSNFGARQRIHTGEKNYTCGECGKCCSQSSSLIIHQRTHTGQKPYQCGECGRSFTNSSHFSAH |
| Parental | RRVHTGENPYKCVDCEKSFNNCTRFREHRRVHSGEKPYGCSQCGRRFSKSSVLTKHREVHVREKLLPPPP |
| .RVHTG.NPYKCVDCEKSFNNC.RFRE.RRVH..EKPY.CSQCGR.FSKS.VL.K.REVH.REKLLPP.P | |
| Retrocopy | QRVHTGKNPYKCVDCEKSFNNCRRFREDRRVHTREKPYRCSQCGRHFSKSFVLIKLREVHIREKLLPPLP |
| Parental | AFCSPENPLKGK |
| .FCSPENPLKGK | |
| Retrocopy | VFCSPENPLKGK |
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 .07 RPM |
| ERP005899_muscle | 0 .00 RPM | 0 .21 RPM |
| SRP017611_brain | 0 .05 RPM | 5 .80 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .71 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .15 RPM |
| SRP030211_testis | 0 .02 RPM | 9 .95 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_270 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_270 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_270 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 | ENSBTAG00000011162 | 1 retrocopy |
retro_btau_270 ,
|
| Otolemur garnettii | ENSOGAG00000009286 | 1 retrocopy |