RetrogeneDB ID: retro_btau_690

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:15551819..15552705(+)
• Located in intron of: ENSBTAG00000014370

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PDLIM1
• Ensembl ID: ENSBTAG00000011182
• Aliases: None
• Description: PDZ and LIM domain protein 1 [Source:RefSeq peptide;Acc:NP_001030532]

Sequence

>retro_btau_690
ATTTCCCAGGTCATTCCTGGAATCAAGGCTGCAATAGCTAATGTATGTGTTGGAGATGTAACCACAGCCACTGATGGGGA
AAATACCAGCAATATATTGTACTTAGAAGCTCAGAACAAAATCAAGGGCTGCACAGACAACATGACTCTCACAGTAGCAA
CAGAACAGAAATATGGTCTCCTCTGGTGACATAGGAAGGGAAACATCACTCATACAAGATGAATTAGCCTCTGAACCCCA
AGAGATCCTACACATAGGAAGCACCCCAAACCAGAGTTCTGCCCTTTACCACCTCACCTTCCTCCAGCTCTCCCCCAGGG
TCGTCACAAACCAGTGCAACAACCCAGTTAGCGTCTACTCCTCTGAAAATATCTAAAACTTTAACAACACCTTGGAGTCA
AAGAGCAGCCAGCAGGCAGATGAACGCAGAGCTTTAGACCATTCTCAGCTTCCAAGCAGACTTGTCTTTGGCAAAGAATC
TGAAGTTTACAAGATGCTTCTGGAGAAACATGAGTTAAATGAGCCTCTGAGACAGCCCACTTCATTCCTGGTTTTGCAGG
AAACCCTGAAGGCTGAGGAGAAAGGGGATCCCAACAAGCCCTCAGGACTCAGAAATGTTAAGGCTCCAGTCACCAAAGTG
GCTACATTGACTAGAAACGCCCAGAAGCTGCTCATGTACGACAAACGTGGCACCGGCACTGTCAGTGTGTTTGTGAAGCT
GCGGGACCGTCACCGCCACCCCGAGTGTTATGTGTGCACCAACTACGGCACCAATCTGAAACAGAAGGGTCATTTCTTTG
TGGAGGATCAGATCTACTGTGGAAAGCACACCCAGGAGCAAGTCACTCCACCAGAGGGCTACGCTGTGATCACCGTGCTC
CCCGAA

Alignment

ORF - retro_btau_690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.09 %
• Parental protein coverage: 91.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ISRVTPGSKAAIGNLCVGDVITAIDGENTSNMTHLEAQNKIKGCTDNMTLTVARSEQK-IWSPLVTEEGK
          IS.V.PG.KAAI.N.CVGDV.TA.DGENTSN...LEAQNKIKGCTDNMTLTVA..EQK.IWSPLVT.EGK
Retrocopy ISQVIPGIKAAIANVCVGDVTTATDGENTSNILYLEAQNKIKGCTDNMTLTVA-TEQK<IWSPLVT*EGK

Parental  RHPYKMN-LASEPQEALHIGSAHNRSAVPFTASPASSSAPRVITNQYNNPAGLYSSENISSFNNALESKT
          .H.YKMN.LASEPQE.LHIGS..N.S...........S.PRV.TNQ.NNP...YSSENI..FNN.LESK.
Retrocopy HHSYKMN<LASEPQEILHIGSTPNQSSALYHLTFLQLS-PRVVTNQCNNPVSVYSSENI*NFNNTLESKS

Parental  AASGQENGRALDHSQLPSGLVIDKESEVYKMLQEKQELNEPPKQSTSFLVLQEILESEEKGDPNKPSGFR
          .....E..RALDHSQLPS.LV..KESEVYKML.EK.ELNEP..Q.TSFLVLQE.L..EEKGDPNKPSG.R
Retrocopy SQQADER-RALDHSQLPSRLVFGKESEVYKMLLEKHELNEPLRQPTSFLVLQETLKAEEKGDPNKPSGLR

Parental  SVKAPVTKVAASIGNAQKLPMCDKCGTGIVGVFVKLRERHRHPECYVCTDCGTNLKQKGHFFVEDQIYCE
          .VKAPVTKVA....NAQKL.M.DK.GTG.V.VFVKLR.RHRHPECYVCT..GTNLKQKGHFFVEDQIYC.
Retrocopy NVKAPVTKVATLTRNAQKLLMYDKRGTGTVSVFVKLRDRHRHPECYVCTNYGTNLKQKGHFFVEDQIYCG

Parental  KHARERVTPPEGYDVITVFPK
          KH..E.VTPPEGY.VITV.P.
Retrocopy KHTQEQVTPPEGYAVITVLPE

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	1.23 RPM	17.45 RPM
ERP005899_muscle	0.00 RPM	120.57 RPM
SRP017611_brain	0.09 RPM	0.87 RPM
SRP017611_kidney	0.00 RPM	20.80 RPM
SRP017611_liver	0.53 RPM	28.84 RPM
SRP030211_testis	0.06 RPM	5.49 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_690 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_690 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_690 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690 ,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558, retro_mmus_779,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819, retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056, retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777, retro_ttru_976,