RetrogeneDB ID: retro_btau_1207

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:13168141..13169146(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSBTAG00000000132
• Aliases: None
• Description: Eukaryotic initiation factor 4A-I [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ54]

Sequence

>retro_btau_1207
GGCCCAGAGGGAATGGACCCCGATGATGTCATCGAGAGCAACTGGAATGAGATTGTTGATAACTTTGATGATATGAACTT
AAAGGAGTCTCTTCTTCGGAGCATCTATGCTTCTGGTTTTGAGAAACCATCAGCTATTCAGCAGAGAGTTATTATTCCAT
GTATTAAAGGTATGATGTGATTGCTCAAGCTCAGTCGGGTACTGGCAAGACAGCCACATTTGCTATTTCCATCCTGCAAC
AGTTGGATATTGAGTTCAAGGAGACCCAAGCACTAGTATTGGCCTCCACTTTTGGATCAACAGATCCAAAAGGTAATTCT
GGCACTTGGAGATTATATAAGAGCAACTTGTCATGCCTGCATTGGTGGAACAAATGTCTGAAATGAAATGCAAAAACTGC
AGGCTGAAGCACCACATATTGTTGTTGGAACACCAGGGAGAGTGTTTGATATGTTAAACAGAAGATATCTCTCTCCAAAA
TAGATCAAAATGTTCATTTTGCATGAAGCAGATGAAATGCTGAGCTGAGGGTTTAAGGATCAAATCTATGAGATTTTCTG
AAAATTAAATACTAGTATTTGGGTGGTGTTGCTTTCTGCCACAATGCCAACGGATGTGTTGGAAGTGACCAAAAAATTCA
TGAAAGATCCAATTCGAATTTTGGTGAAAAAAGAAGAATTGACCTTTGAAGGAATCAAACAGTTTTATATTAATGTTGAA
AGAAGGGAATGGAAGTTGGATACACTTTATGACTTGTACGAGACACTGACAATTACACAGGCTGTTATTTTTCTCAATAC
AAGGTGCAAGGTGGACTGGCTCACAGAGAAAATGCATGCCAGGTACTTCACAGTTTCTGCCCTGCGTGGTGACATGGGCC
AGAAAGAAAGAGATGTTATCATGAGGGAATTTCGACCAGGGTCAAGCCATGTTCTGATCACTACTGACTTGTTGGCTTGT
GGAATTGATGTGCAACAAGTGTCATTGGTTATAAACTATGATCTA

Alignment

ORF - retro_btau_1207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.12 %
• Parental protein coverage: 83. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKG-YDVIAQAQSGTG
          GP.GM.P..VIESNWNEIVD.FDDMNL.ESLLR.IYA.GFEKPSAIQQR.I.PCIKG.YDVIAQAQSGTG
Retrocopy GPEGMDPDDVIESNWNEIVDNFDDMNLKESLLRSIYASGFEKPSAIQQRVIIPCIKG<YDVIAQAQSGTG

Parental  KTATFAISILQQIELDLKATQALVLAPTRE-LAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQME
          KTATFAISILQ...LD........L......L.QQIQKV..ALGDY..A.CHACIGGTNV..E.QKLQ.E
Retrocopy KTATFAISILQ--QLDIEFKETQALVLAST>LDQQIQKVILALGDYIRATCHACIGGTNV*NEMQKLQAE

Parental  APHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDV
          APHI.VGTPGRVFDMLNRRYLSPK.IKMF.L.EADEMLS.GFKDQIY.IF.KLN....VVLLSATMP.DV
Retrocopy APHIVVGTPGRVFDMLNRRYLSPK*IKMFILHEADEMLS*GFKDQIYEIF*KLNTSIWVVLLSATMPTDV

Parental  LEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTE
          LEVTKKFM.DPIRILVKKEELT.EGI.QFYINVER.EWKLDTL.DLYETLTITQAVIF.NTR.KVDWLTE
Retrocopy LEVTKKFMKDPIRILVKKEELTFEGIKQFYINVERREWKLDTLYDLYETLTITQAVIFLNTRCKVDWLTE

Parental  KMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL
          KMHAR.FTVSA..GDM.QKERDVIMREFR.GSS.VLITTDLLA.GIDVQQVSLVINYDL
Retrocopy KMHARYFTVSALRGDMGQKERDVIMREFRPGSSHVLITTDLLACGIDVQQVSLVINYDL

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	63.66 RPM
ERP005899_muscle	0.00 RPM	224.41 RPM
SRP017611_brain	0.05 RPM	78.48 RPM
SRP017611_kidney	0.06 RPM	145.87 RPM
SRP017611_liver	0.08 RPM	120.28 RPM
SRP030211_testis	0.05 RPM	141.06 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1207 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1207 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000132	1 retrocopy	retro_btau_1207 ,
Bos taurus	ENSBTAG00000014724	2 retrocopies	retro_btau_258, retro_btau_522,
Loxodonta africana	ENSLAFG00000001107	1 retrocopy	retro_lafr_1210,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Oryctolagus cuniculus	ENSOCUG00000010375	5 retrocopies	retro_ocun_1020, retro_ocun_1326, retro_ocun_1375, retro_ocun_475, retro_ocun_934,
Pongo abelii	ENSPPYG00000007926	7 retrocopies	retro_pabe_1090, retro_pabe_1474, retro_pabe_3759, retro_pabe_3792, retro_pabe_548, retro_pabe_846, retro_pabe_987,