RetrogeneDB ID: retro_btau_1687

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:96440861..96441227(+)
• Located in intron of: ENSBTAG00000010838

Retrocopy information

• Ensembl ID: ENSBTAG00000045898
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SKP1
• Ensembl ID: ENSBTAG00000025191
• Aliases: SKP1, SKP1A
• Description: S-phase kinase-associated protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZCF3]

Sequence

>retro_btau_1687
ATGCCTTCCATTAAGTTACAGAGTTCTGATGGAGAGATATTCAAAGTTGATATTGAAATCGCAAAACAGTCTGTGACCAT
CAAGACTACGTTGGAAGATTTGGGAATGGGTGATGAAGGAGATGATGATCCAGTCCCCTTGACAAATGTTAATGCAGCAA
TATTAGAAAAGGTCGTTCAGTGGTGCGCCCACCACAAGGATGACCCTCCTCCTCCTGAGGATGATGAGAACAAAGGAAAA
TGAGCAGATGATATACCTGTTTGGGATCAAGCATTCCTGAAAGTTGACCAAGGGACACTCTTTGAGCTTATATTGGCAGC
AAACTACTTAGACATTAAAGGTTTGCTTGATGTTACCTGCAAGACT

Alignment

ORF - retro_btau_1687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.16 %
• Parental protein coverage: 74.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPP
          MPSIKLQSSDGEIF.VD.EIAKQSVTIKT.LEDLGM.DEGDDDPVPL.NVNAAIL.KV.QWC.HHKDDPP
Retrocopy MPSIKLQSSDGEIFKVDIEIAKQSVTIKTTLEDLGMGDEGDDDPVPLTNVNAAILEKVVQWCAHHKDDPP

Parental  PPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKT
          PPEDDENK.K..DDIPVWDQ.FLKVDQGTLFELILAANYLDIKGLLDVTCKT
Retrocopy PPEDDENKGK*ADDIPVWDQAFLKVDQGTLFELILAANYLDIKGLLDVTCKT

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	0.58 RPM	77.36 RPM
ERP005899_muscle	0.48 RPM	77.18 RPM
SRP017611_brain	0.09 RPM	89.03 RPM
SRP017611_kidney	0.06 RPM	70.00 RPM
SRP017611_liver	0.60 RPM	24.77 RPM
SRP030211_testis	0.48 RPM	128.22 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1687 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1687 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025191	5 retrocopies	retro_btau_10, retro_btau_1062, retro_btau_1253, retro_btau_1444, retro_btau_1687 ,
Canis familiaris	ENSCAFG00000000994	5 retrocopies	retro_cfam_1613, retro_cfam_779, retro_cfam_813, retro_cfam_889, retro_cfam_965,
Callithrix jacchus	ENSCJAG00000013613	1 retrocopy	retro_cjac_112,
Echinops telfairi	ENSETEG00000007560	5 retrocopies	retro_etel_1730, retro_etel_515, retro_etel_758, retro_etel_762, retro_etel_811,
Homo sapiens	ENSG00000113558	10 retrocopies	retro_hsap_2193, retro_hsap_2596, retro_hsap_3321, retro_hsap_3346, retro_hsap_3863, retro_hsap_4161, retro_hsap_4163, retro_hsap_4164, retro_hsap_724, retro_hsap_972,
Gorilla gorilla	ENSGGOG00000022930	7 retrocopies	retro_ggor_1288, retro_ggor_1300, retro_ggor_2601, retro_ggor_2602, retro_ggor_2796, retro_ggor_2797, retro_ggor_778,
Latimeria chalumnae	ENSLACG00000016599	1 retrocopy	retro_lcha_103,
Loxodonta africana	ENSLAFG00000016832	1 retrocopy	retro_lafr_83,
Microcebus murinus	ENSMICG00000017588	3 retrocopies	retro_mmur_270, retro_mmur_803, retro_mmur_997,
Myotis lucifugus	ENSMLUG00000022919	13 retrocopies	retro_mluc_1455, retro_mluc_1738, retro_mluc_1895, retro_mluc_2009, retro_mluc_2260, retro_mluc_2261, retro_mluc_2520, retro_mluc_2527, retro_mluc_2557, retro_mluc_267, retro_mluc_383, retro_mluc_841, retro_mluc_944,
Monodelphis domestica	ENSMODG00000014168	4 retrocopies	retro_mdom_1173, retro_mdom_155, retro_mdom_1648, retro_mdom_929,
Otolemur garnettii	ENSOGAG00000028707	8 retrocopies	retro_ogar_1446, retro_ogar_1510, retro_ogar_1511, retro_ogar_1890, retro_ogar_2019, retro_ogar_2728, retro_ogar_3306, retro_ogar_581,
Pongo abelii	ENSPPYG00000015783	7 retrocopies	retro_pabe_1915, retro_pabe_199, retro_pabe_2072, retro_pabe_2736, retro_pabe_2756, retro_pabe_626, retro_pabe_824,
Rattus norvegicus	ENSRNOG00000005828	6 retrocopies	retro_rnor_1391, retro_rnor_1392, retro_rnor_1465, retro_rnor_1888, retro_rnor_2166, retro_rnor_2333,