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 symbol: ZKSCAN2
• Ensembl ID: ENSBTAG00000011162
• Aliases: None
• Description: zinc finger protein with KRAB and SCAN domains 2 [Source:RefSeq peptide;Acc:NP_001192599]

Sequence

>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

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_270 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_270 was not experimentally validated.

Homology

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	retro_ogar_2080,