RetrogeneDB ID: retro_btau_971

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 22:20199548..20199999(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSEN15
• Ensembl ID: ENSBTAG00000016369
• Aliases: TSEN15, C16H1ORF19
• Description: tRNA-splicing endonuclease subunit Sen15 [Source:RefSeq peptide;Acc:NP_001069780]

Sequence

>retro_btau_971
GGCGGCGATTGCGGTGGCGGCAGCGCCCACCCACGGGCCCCCCGAGGACACCTGGATGGGCACGCACCCTAAGTATTTAG
AAATGATGGAGTTAATTATAAGAGATGCCACCCAAGCTTATACAGCGTTCTTGGCTTGCCTGGACCTCATAGTGAGTAAA
AGCTGGCATGAAGTAAACTGTGTGGGATTACTAGATCTCCAGCTCATCCACCTTCTCAGCACTGAGACAGAAGCAGAAGG
GTTTACAGTCTGTGGTACCTACGCCCATCAGTGCTTCCCTCAGCCATAACAGGATAAGGGGGATCTTGAAGGCATCCTGA
AAATAGCAAGGTGATCCCGATTGCCTATGTCTTTTACTTTGGCCATAGTGGAGTCTGACTCCACAACAGTCTACTACAAA
CTCACTGATGGATTTATGCTGCCAGATCCTAAGAATATTTCCCTTAGAAGA

Alignment

ORF - retro_btau_971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 89.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GDDRGGGSAHPWAP-EDAWMGTHPKYLEMMELDIGDATQVYIAFLVYLDLMESKSWHEVNCVGLPDLQLI
          G.D.GGGSAHP.AP.ED.WMGTHPKYLEMMEL.I.DATQ.Y.AFL..LDL..SKSWHEVNCVGL.DLQLI
Retrocopy GGDCGGGSAHPRAP>EDTWMGTHPKYLEMMELIIRDATQAYTAFLACLDLIVSKSWHEVNCVGLLDLQLI

Parental  CLLGTEIEGE-GLQTVVPTPISASLSHNRIREILKASRKLQGDPD-LPTSFTLAIVESDSTIVYYKLTDG
          .LL.TE.E.E.GLQ.VVPTPISASLSHNRIR.ILKAS.K.QGDPD.LP.SFTLAIVESDST.VYYKLTDG
Retrocopy HLLSTETEAE>GLQSVVPTPISASLSHNRIRGILKAS*K*QGDPD<LPMSFTLAIVESDSTTVYYKLTDG

Parental  FMLPDPQNISLRR
          FMLPDP.NISLRR
Retrocopy FMLPDPKNISLRR

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	33.74 RPM
ERP005899_muscle	0.00 RPM	7.76 RPM
SRP017611_brain	0.00 RPM	23.11 RPM
SRP017611_kidney	0.00 RPM	16.54 RPM
SRP017611_liver	0.00 RPM	8.83 RPM
SRP030211_testis	0.00 RPM	14.47 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_971 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_971 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_971 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016369	1 retrocopy	retro_btau_971 ,
Callithrix jacchus	ENSCJAG00000005356	1 retrocopy	retro_cjac_3055,
Dasypus novemcinctus	ENSDNOG00000017611	2 retrocopies	retro_dnov_1176, retro_dnov_2529,
Homo sapiens	ENSG00000198860	1 retrocopy	retro_hsap_1721,
Gorilla gorilla	ENSGGOG00000015804	2 retrocopies	retro_ggor_2267, retro_ggor_240,
Loxodonta africana	ENSLAFG00000014109	1 retrocopy	retro_lafr_684,
Macaca mulatta	ENSMMUG00000016409	1 retrocopy	retro_mmul_1214,
Mustela putorius furo	ENSMPUG00000011790	1 retrocopy	retro_mputfur_1261,
Mus musculus	ENSMUSG00000014980	1 retrocopy	retro_mmus_2721,
Nomascus leucogenys	ENSNLEG00000018024	1 retrocopy	retro_nleu_98,
Otolemur garnettii	ENSOGAG00000003128	1 retrocopy	retro_ogar_3264,
Pongo abelii	ENSPPYG00000000421	4 retrocopies	retro_pabe_1436, retro_pabe_3065, retro_pabe_3196, retro_pabe_469,
Pan troglodytes	ENSPTRG00000023202	2 retrocopies	retro_ptro_1229, retro_ptro_147,
Pteropus vampyrus	ENSPVAG00000001103	1 retrocopy	retro_pvam_1458,
Ictidomys tridecemlineatus	ENSSTOG00000013230	2 retrocopies	retro_itri_1538, retro_itri_1849,
Vicugna pacos	ENSVPAG00000002941	2 retrocopies	retro_vpac_381, retro_vpac_565,