RetrogeneDB ID: retro_btau_277

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:109955678..109956312(+)
• Located in intron of: ENSBTAG00000031561

Retrocopy information

• Ensembl ID: ENSBTAG00000047963
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.94621
• Ensembl ID: ENSBTAG00000021580
• Aliases: HNRNPA3, HNRPA3
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:RefSeq peptide;Acc:NP_001192358]

Sequence

>retro_btau_277
CCCCAGCTCGACTCCGGCCATGGCCGCCGCTGCCGAGGGGAGAAGGGTCATGATCTCAAGCAACAGGAGCAGTTGAGAAA
GCTGTTTATTGGCAGTCTGAGCTTTGAAACTACAGATGATAGCTTAAGAGAACATTTTGAGATGGGGCACACTTACAGAT
TGTGTGGTGATGAGAGACCCCCCAAACAAAATGTTCCAGGGGCTTTGGTTTTGTGACTTGTTCTTGTGTTGAAGAAGTGG
ATGCAAAATGTGTGCTCGACCACACAAGGTTGATGGGCATGTAATAGAACCAAAGAGAGCTGTTTCTAGAAAGGATTCTG
TAAAGCCTGGTGCCCATCTAACAGTGAAGAAAATTTTTGTTGGTGGTATTAAAGAAGATACAGAAGAATGTAATTTGAGA
GACTACTTTAAAAAGTATGGCAAGACTGAAACCATAGAAGTTATGGAAGACAGGCAGAGTGGGAAAAAGAGAGGATTTGC
TTTTGGAACTTTTGATGATCATGGTACAGTTGATAAAATTGTTGTTCAGAAATACCACACTATTAATGGGCATAATTGTG
AAGTGAAAAAGGCCCTTTCTAAACAAGAGATGCAATCTGCTGCATCACAAAGAGGTCATAGAGGTGGATCTGGC

Alignment

ORF - retro_btau_277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.18 %
• Parental protein coverage: 55.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PQPDSGRRRRRRGAQGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMR-DPQTKRSRGF
          PQ.DSG..RR.RG..GHD.K..EQLRKLFIG.LSFETTDDSLREHFE...T...C...R..PQTK.SRGF
Retrocopy PQLDSGHGRRCRGEKGHDLKQQEQLRKLFIGSLSFETTDDSLREHFEMGHTYRLCGDER<TPQTKCSRGF

Parental  GFVTYSCVEEVDA-AMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFE
          GFVT.SCVEEVDA..MCARPHKVDG.V.EPKRAVSR.DSVKPGAHLTVKKIFVGGIKEDTEE.NLRDYF.
Retrocopy GFVTCSCVEEVDA<KMCARPHKVDGHVIEPKRAVSRKDSVKPGAHLTVKKIFVGGIKEDTEECNLRDYFK

Parental  KYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRG
          KYGK.ETIEVMEDRQSGKKRGFAF.TFDDH.TVDKIVVQKYHTINGHNCEVKKALSKQEMQSA.SQRG..
Retrocopy KYGKTETIEVMEDRQSGKKRGFAFGTFDDHGTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAASQRGHR

Parental  GGSG
          GGSG
Retrocopy GGSG

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	25.74 RPM
ERP005899_muscle	0.05 RPM	150.66 RPM
SRP017611_brain	0.00 RPM	85.83 RPM
SRP017611_kidney	0.00 RPM	139.41 RPM
SRP017611_liver	0.00 RPM	61.16 RPM
SRP030211_testis	0.03 RPM	187.58 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_277 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_277 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 87 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001553	20 retrocopies	retro_btau_1019, retro_btau_1065, retro_btau_1268, retro_btau_1378, retro_btau_1379, retro_btau_1437, retro_btau_1455, retro_btau_1657, retro_btau_1673, retro_btau_283, retro_btau_337, retro_btau_403, retro_btau_462, retro_btau_516, retro_btau_519, retro_btau_589, retro_btau_602, retro_btau_677, retro_btau_715, retro_btau_822,
Bos taurus	ENSBTAG00000005726	4 retrocopies	retro_btau_1330, retro_btau_1535, retro_btau_193, retro_btau_228,
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461,
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277 , retro_btau_370, retro_btau_811, retro_btau_90,
Dasypus novemcinctus	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens	ENSG00000170144	11 retrocopies	retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,