RetrogeneDB ID: retro_btau_1348

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:48369023..48369367(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL22
• Ensembl ID: ENSBTAG00000019457
• Aliases: None
• Description: 39S ribosomal protein L22, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q3SZX5]

Sequence

>retro_btau_1348
AAAATTGTGTATTCTTCACAACTACCTGGAGAACTTTCTCAGATACCAGCTGAAATCTACCATTGTTGAAGACAAAGTAC
AGCAAAGATGTGGTATTTGGGAAAATTGATATGAGGAATGTCCTTTGACCAGGCTTTGGCTCAACTGGAATTCAGTGACC
AAAAAACAGGGGCCCCAATAATGAAAGAGGTTCTCTTAAAAGCCCAAGATATAGCAGTGGGAGATCACAATGTGGAGTTC
AGATCCAACTTATATATGGCTAAGTCCACTTCAGGGCAAGGCCAGTACTTGATACACATTGATATCAGCATGGAGGTGGC
TTTGGGATCATGGGATTATTTTGT

Alignment

ORF - retro_btau_1348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 57.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KIVYPPQLPGEPRR-PAEIYHCRRQIKYSKDKMWYLAKLIRGMSIDQALAQLEFSDKK-GAQIIKEVLLE
          KIVY..QLPGE....PAEIYHC.RQ...S..KMWYL.KLI.GMS.DQALAQLEFSD.K.GA.I.KEVLL.
Retrocopy KIVYSSQLPGELSQIPAEIYHC*RQ---STAKMWYLGKLI*GMSFDQALAQLEFSDQKTGAPIMKEVLLK

Parental  AQDMAVRDHNVEFRSNLYIAESTSGRGQYLKRIR-YHGRGRFGIMEKVFC
          AQD.AV.DHNVEFRSNLY.A.STSG.GQYL..I..Y...G.FGIM...FC
Retrocopy AQDIAVGDHNVEFRSNLYMAKSTSGQGQYLIHID<YQHGGGFGIM-GLFC

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	13.12 RPM
ERP005899_muscle	0.00 RPM	11.19 RPM
SRP017611_brain	0.00 RPM	5.98 RPM
SRP017611_kidney	0.00 RPM	19.26 RPM
SRP017611_liver	0.00 RPM	6.27 RPM
SRP030211_testis	0.14 RPM	34.77 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1348 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1348 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003875	1 retrocopy	retro_acar_88,
Bos taurus	ENSBTAG00000019457	1 retrocopy	retro_btau_1348 ,
Canis familiaris	ENSCAFG00000017605	2 retrocopies	retro_cfam_1456, retro_cfam_584,
Macaca mulatta	ENSMMUG00000021229	1 retrocopy	retro_mmul_1889,
Otolemur garnettii	ENSOGAG00000016777	1 retrocopy	retro_ogar_1042,
Vicugna pacos	ENSVPAG00000001170	1 retrocopy	retro_vpac_294,