RetrogeneDB ID: retro_btau_1572

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:41508462..41509351(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FYTTD1
• Ensembl ID: ENSBTAG00000014874
• Aliases: None
• Description: UAP56-interacting factor [Source:UniProtKB/Swiss-Prot;Acc:Q17QU6]

Sequence

>retro_btau_1572
CCGAAAGCCCGCAGCAATGAAAACCTGGACAGAATTGATGTGTCTTAGGACGATATCATCAAACTGAATCGAAAGGAAGG
AAAGAAGCAGAATTTCCTGAGATTAAATAGAAGTCTTCAGCAAAGTGGTGCCAGGCAATTCAGAATGAGAGTAAGATGGG
CTATTCAATAGAACTCTGGTTTTGGTAAGAATAGTCTGAGCCGTAGAAGAAGAGTGACGCCTGGGAATAGACGTCCTTAT
GGAGTTATCACTGGCCTTGCATCTAGGAAAGCAACTGGAATTCGAAAGGGAATTAGTCCTATGAATCGACCACCTTTAAG
TGGCAAGAATACAGAATGATATTTTCCAACATTAAAAAGGAAGGCAAATCTGAGACTAAATGAATACTGCAGGCATAACC
AGTTGCAGCTCTCAAGAGACCTAACCAGTTAAATAGAAAAAATTACATTCCAGCCGGTTTTACCAGGAGTGGAAATAAAT
TAAGTCATCAGAAAGACACTAATCAGGGAGCTTTTCTTTTCAGAAGAGGCCTGAAGGTTCAGGCCCAGTTGAACTCAGAA
CAACTGCTAGACGATGTAGTAGCAAAGAGAACTCATCAATAGAGAACTTCTACCACAAATGGAGGAATTTTGACTGTATC
CATTGATAATCCAGGAGCAGCTCAGTGCCCAGTAACTCAGAAACCACGATCAACTCGTACTGCTGTGCCCTCATTCTTGA
CAAAACGGGATCAATCTGATGTAAAGAAAGTTCCTAAAGGTGTCACTCTACAATTTGAAATAAACAGTGTTGGAAAAAGA
CGGGGATGACTTTGAATGAGCGATTTGGGATCCTGAAGGGACAGAGAGCCATTTTCAACAAAGGAGGTAGCTGCTTTGTA
ACTGTGGGA

Alignment

ORF - retro_btau_1572 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.39 %
• Parental protein coverage: 94.03 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKARSNENLDKIDMSLDDIIKLNRKEGKKQNFPRLNRRLQQSSARQFRMRVRWGIQQNSGFGKNSLSRRG
          PKARSNENLD.ID.S.DDIIKLNRKEGKKQNF.RLNR.LQQS.ARQFRMRVRW.IQ.NSGFGKNSLSRR.
Retrocopy PKARSNENLDRIDVS*DDIIKLNRKEGKKQNFLRLNRSLQQSGARQFRMRVRWAIQ*NSGFGKNSLSRRR

Parental  RVMPGKRRPYGVITGLAARKATGIRKGISPMNRPPLSDKNIERYFPAL-KRKANLLRQNEVQRKPVAALK
          RV.PG.RRPYGVITGLA.RKATGIRKGISPMNRPPLS.KN.E.YFP.L.K...........Q..PVAALK
Retrocopy RVTPGNRRPYGVITGLASRKATGIRKGISPMNRPPLSGKNTE*YFPTL<KKEGKSETK*ILQA*PVAALK

Parental  RPNQLNRKNNIPNNFTRSGNKLSHQKDTRQATFLFRRGLKVQAQLNSEQLLDDVVAKRTRQWRTSTTNGG
          RPNQLNRKN.IP..FTRSGNKLSHQKDT.Q..FLFRRGLKVQAQLNSEQLLDDVVAKRT.Q.RTSTTNGG
Retrocopy RPNQLNRKNYIPAGFTRSGNKLSHQKDTNQGAFLFRRGLKVQAQLNSEQLLDDVVAKRTHQ*RTSTTNGG

Parental  ILTVSIDNPGAVQCPVTQKPRLTRTAVPSFLTKRDQSDIKKVPKGVPLQFDINSVG-KQTGMTLNERFGI
          ILTVSIDNPGA.QCPVTQKPR.TRTAVPSFLTKRDQSD.KKVPKGV.LQF.INSVG.K.TGMTLNERFGI
Retrocopy ILTVSIDNPGAAQCPVTQKPRSTRTAVPSFLTKRDQSDVKKVPKGVTLQFEINSVG<KKTGMTLNERFGI

Parental  LKEQRATLTFNKGGSRFVTVG
          LK.QRA...FNKGGS.FVTVG
Retrocopy LKGQRA--IFNKGGSCFVTVG

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	10.81 RPM
ERP005899_muscle	0.00 RPM	18.42 RPM
SRP017611_brain	0.05 RPM	17.91 RPM
SRP017611_kidney	0.00 RPM	28.98 RPM
SRP017611_liver	0.00 RPM	10.27 RPM
SRP030211_testis	0.01 RPM	76.87 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1572 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1572 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1572 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572 ,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639, retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039, retro_cpor_586,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,