RetrogeneDB ID: retro_btau_1016

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:2596485..2596940(-)
• Located in intron of: ENSBTAG00000007937

Retrocopy information

• Ensembl ID: ENSBTAG00000047911
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS7
• Ensembl ID: ENSBTAG00000016224
• Aliases: None
• Description: 40S ribosomal protein S7 [Source:UniProtKB/Swiss-Prot;Acc:A6H769]

Sequence

>retro_btau_1016
TCCAGGCCCAGCAGGATTGTGAAGCCCAGTGGTGAGAAGCCCCCTGAGTTTGAGTTGGGCATCTCCCAGGCCCTCCTGGA
GCTGGAGATGAACTTGGACCTCAGGGCCCAGCTGCAGAAGCTGAACATCATGGCCACCAAGGAAATTGAAGTTGGTGGTG
GTCAGAAAGGTATCATAATCTTTGTTCCCGTTCCTCAACTGAAATTTCTCCAGAAAATTCAGGTCCTGTGGTATGTGAGC
TGGAGAAGTTCAGTGGGAAGCGCGTTGTCTTTATTGCTCAGACGAGAATTCTGCCTAAGCAAACTCGAAAAAGCTGTACA
AAAAACAAGCAAAAACTTCCCAGGAGCTGCACACTGGTAGCTTTGCATGACACCATCCTGGAGGACTTGGTTTTCCCAAG
TGAGATTGTGGGCAGGAAAATCCACATGAAGCCAGATGGCAGGCAGCTCGTAAAG

Alignment

ORF - retro_btau_1016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 78.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLKSF
          S....IVKP.GEKP.EFE.GISQALLELEMN.DL.AQL..LNI.A.KEIEVGGG.K.IIIFVPVPQLK..
Retrocopy SRPSRIVKPSGEKPPEFELGISQALLELEMNLDLRAQLQKLNIMATKEIEVGGGQKGIIIFVPVPQLKFL

Parental  QKIQV-RLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVG
          QKIQV...V.ELE.KFSGK.VVFIAQ.RILPK.TRKS.TKNKQK.PRS.TL.A.HD.ILEDLVFPSEIVG
Retrocopy QKIQV<PVVCELE-KFSGKRVVFIAQTRILPKQTRKSCTKNKQKLPRSCTLVALHDTILEDLVFPSEIVG

Parental  KRIRVKLDGSRLIK
          ..I..K.DG..L.K
Retrocopy RKIHMKPDGRQLVK

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	101.22 RPM
ERP005899_muscle	0.00 RPM	1274.70 RPM
SRP017611_brain	0.00 RPM	159.24 RPM
SRP017611_kidney	0.00 RPM	356.76 RPM
SRP017611_liver	0.00 RPM	195.26 RPM
SRP030211_testis	0.00 RPM	352.76 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1016 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1016 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1016 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016224	5 retrocopies	retro_btau_1016 , retro_btau_1046, retro_btau_1351, retro_btau_448, retro_btau_997,
Canis familiaris	ENSCAFG00000003263	1 retrocopy	retro_cfam_1798,
Callithrix jacchus	ENSCJAG00000016462	2 retrocopies	retro_cjac_16, retro_cjac_2287,
Cavia porcellus	ENSCPOG00000009795	2 retrocopies	retro_cpor_1139, retro_cpor_773,
Felis catus	ENSFCAG00000023243	2 retrocopies	retro_fcat_1534, retro_fcat_41,
Gorilla gorilla	ENSGGOG00000023095	13 retrocopies	retro_ggor_2028, retro_ggor_2090, retro_ggor_2161, retro_ggor_218, retro_ggor_2452, retro_ggor_2927, retro_ggor_294, retro_ggor_2965, retro_ggor_3047, retro_ggor_346, retro_ggor_400, retro_ggor_484, retro_ggor_597,
Loxodonta africana	ENSLAFG00000015087	11 retrocopies	retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus	ENSMLUG00000006121	1 retrocopy	retro_mluc_1118,
Mus musculus	ENSMUSG00000061477	2 retrocopies	retro_mmus_271, retro_mmus_53,
Oryctolagus cuniculus	ENSOCUG00000008507	2 retrocopies	retro_ocun_203, retro_ocun_230,
Otolemur garnettii	ENSOGAG00000028165	1 retrocopy	retro_ogar_133,
Pongo abelii	ENSPPYG00000025872	12 retrocopies	retro_pabe_1033, retro_pabe_1555, retro_pabe_2506, retro_pabe_2982, retro_pabe_2983, retro_pabe_31, retro_pabe_313, retro_pabe_360, retro_pabe_3659, retro_pabe_3803, retro_pabe_499, retro_pabe_524,
Pan troglodytes	ENSPTRG00000011615	3 retrocopies	retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Pteropus vampyrus	ENSPVAG00000002071	7 retrocopies	retro_pvam_1051, retro_pvam_1183, retro_pvam_1330, retro_pvam_1437, retro_pvam_207, retro_pvam_543, retro_pvam_887,
Rattus norvegicus	ENSRNOG00000008551	2 retrocopies	retro_rnor_39, retro_rnor_391,