RetrogeneDB ID: retro_btau_13

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:73186222..73186471(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000017330
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IER3IP1
• Ensembl ID: ENSBTAG00000032961
• Aliases: None
• Description: Immediate early response 3-interacting protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q1JQC2]

Sequence

>retro_btau_13
ATGGCTTTTACGTTGTATTCGCTGCTGCAGGCGGCCCTTCTCTGCGTCAATGCCATCGCCGTGCTTCACGAGGAGCGTTT
CCTCAAGAACATTGGCTGGGGAACAGACCAGGGAATTGGAGGATTCGGAGAAGAGCCAGGAATTAAATCTCAGCTAATGA
ACCTTATTCGATCTGTAAGAACCGTGATGAGAGTGCCATTGATAATAGTAAACTCAATTGCAATTGTATTACTTTTACTG
TTTGGGTGA

Alignment

ORF - retro_btau_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFTLYSLLQAALLCVNAIAVLHEERFLKNIGWGTDQGIGGFGEEPGIKSQLMNLIRSVRTVMRVPLIIV
          MAFTLYSLLQAALLCVNAIAVLHEERFLKNIGWGTDQGIGGFGEEPGIKSQLMNLIRSVRTVMRVPLIIV
Retrocopy MAFTLYSLLQAALLCVNAIAVLHEERFLKNIGWGTDQGIGGFGEEPGIKSQLMNLIRSVRTVMRVPLIIV

Parental  NSIAIVLLLLFG
          NSIAIVLLLLFG
Retrocopy NSIAIVLLLLFG

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	0.22 RPM	26.17 RPM
ERP005899_muscle	0.16 RPM	32.25 RPM
SRP017611_brain	0.05 RPM	8.04 RPM
SRP017611_kidney	0.06 RPM	13.75 RPM
SRP017611_liver	0.00 RPM	10.80 RPM
SRP030211_testis	0.74 RPM	20.39 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_13 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_13 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000032961	1 retrocopy	retro_btau_13 ,
Callithrix jacchus	ENSCJAG00000004610	1 retrocopy	retro_cjac_3333,
Echinops telfairi	ENSETEG00000000303	1 retrocopy	retro_etel_1526,
Homo sapiens	ENSG00000134049	1 retrocopy	retro_hsap_1156,
Gorilla gorilla	ENSGGOG00000027939	1 retrocopy	retro_ggor_903,
Mus musculus	ENSMUSG00000090000	1 retrocopy	retro_mmus_150,
Nomascus leucogenys	ENSNLEG00000011450	1 retrocopy	retro_nleu_2504,
Otolemur garnettii	ENSOGAG00000016626	1 retrocopy	retro_ogar_2152,
Pongo abelii	ENSPPYG00000009141	3 retrocopies	retro_pabe_2850, retro_pabe_2851, retro_pabe_962,
Pan troglodytes	ENSPTRG00000010002	1 retrocopy	retro_ptro_791,
Tupaia belangeri	ENSTBEG00000001443	4 retrocopies	retro_tbel_1530, retro_tbel_2783, retro_tbel_3343, retro_tbel_3429,
Tursiops truncatus	ENSTTRG00000001019	1 retrocopy	retro_ttru_1930,