RetrogeneDB ID: retro_btau_722

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:49080572..49080929(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS19
• Ensembl ID: ENSBTAG00000011963
• Aliases: None
• Description: 40S ribosomal protein S19 [Source:UniProtKB/Swiss-Prot;Acc:Q32PD5]

Sequence

>retro_btau_722
AAAGTCCGGGAAGCTGAATGGGTGGACACCGTCAAGCTGGCCAAGCATAAAGAACTTGCTCCCTACGATGAGAACTGGTT
CTACACACGAGCTGCTTCCACGGCACGGCACCTGTACCTCCCGGGTGGCGCTGGGGTTGGCTCCATGACCAAGATCTATG
GGGGGTGCCAGAGGAACGGTGTCATGCCCAGCCACTTCAGCAGAGGCTCCAAGAGTGTGGCCCGGCGGGTCCTCCAAGCC
CTGGAGGGGCTGAAAATGGTGGAAAAGGACCAAGATGGGGGCCGCAAACTGACGCCTCAGGGACAGAGAGATCTGGACAG
AATCGCTGGACAGGTGGCAGCTGCCAACAAGAAGCAT

Alignment

ORF - retro_btau_722 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.96 %
• Parental protein coverage: 82.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGS
          K....EWVDTVKLAKHKELAPYDENWFYTRAASTARHLYL.GGAGVGSMTKIYGG.QRNGVMPSHFSRGS
Retrocopy KVREAEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLPGGAGVGSMTKIYGGCQRNGVMPSHFSRGS

Parental  KSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANKKH
          KSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANKKH
Retrocopy KSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANKKH

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	0.14 RPM	34.75 RPM
ERP005899_muscle	1.16 RPM	852.02 RPM
SRP017611_brain	0.18 RPM	79.48 RPM
SRP017611_kidney	0.24 RPM	148.24 RPM
SRP017611_liver	0.08 RPM	103.98 RPM
SRP030211_testis	0.12 RPM	105.08 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_722 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_722 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_722 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011963	2 retrocopies	retro_btau_722 , retro_btau_77,
Canis familiaris	ENSCAFG00000028485	10 retrocopies	retro_cfam_1017, retro_cfam_1074, retro_cfam_1155, retro_cfam_1251, retro_cfam_1377, retro_cfam_149, retro_cfam_1998, retro_cfam_2212, retro_cfam_249, retro_cfam_499,
Callithrix jacchus	ENSCJAG00000020243	5 retrocopies	retro_cjac_1968, retro_cjac_2004, retro_cjac_2094, retro_cjac_2324, retro_cjac_3,
Dasypus novemcinctus	ENSDNOG00000002376	4 retrocopies	retro_dnov_1084, retro_dnov_1124, retro_dnov_1838, retro_dnov_2456,
Erinaceus europaeus	ENSEEUG00000013614	4 retrocopies	retro_eeur_252, retro_eeur_259, retro_eeur_318, retro_eeur_385,
Monodelphis domestica	ENSMODG00000010067	3 retrocopies	retro_mdom_1531, retro_mdom_1888, retro_mdom_883,
Rattus norvegicus	ENSRNOG00000048199	3 retrocopies	retro_rnor_221, retro_rnor_299, retro_rnor_51,
Sus scrofa	ENSSSCG00000003042	3 retrocopies	retro_sscr_1064, retro_sscr_308, retro_sscr_58,