RetrogeneDB ID: retro_btau_1498

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:72705784..72706450(-)
• Located in intron of: ENSBTAG00000001772

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSBTAG00000010598
• Aliases: None
• Description: eukaryotic translation initiation factor 4E type 2 isoform 1 [Source:RefSeq peptide;Acc:NP_001069263]

Sequence

>retro_btau_1498
ATGAACAACAAGTTCGACGCATTGAAAGATGATGACAGTGGGGACCATGATCAGAATGAAGAAAACAGCACACAGAAAGA
TGGTGAGAAGGAAAAAACGGAACGAGACAAGAGTCAGAGCAGCAGCAAGAGGAAGGCTGTCGTCCCTGGGCCGGCCGAGC
ACCCCCTGCAGTATAACTACACTTTTTGGTACTCCAGGAGAACCCCCGGCCGTCCCACCAGCTCACAGAGCTATGAACAG
AATATCAAACAGATTGGCACCTTTGCCTCTGTGGAGCAGTTCTGGAGGTTTTACAGCCACATGGTGCGTCCCGGGGACTT
GACAGGCCACAGCGACTTCCATCTCTTCAAAGAAGGAATTAAACCCATGTGGGAGGATGATGCAAATAAAAATGGCGGAA
AGTGGATAATTCGACTGCGGAAGGGCTTGGCATCCCGCTGCTGGGAGAATCTCATCTTGGCTATGCTGGGGGAACAGTTC
ATGGTTGGGGAGGAGATCTGCGGGGCTGTGGTCTCTGTCCGCTTTCAGGAGGACATTATTTCCATATGGAATAAGACTGC
CAGCGATCAAGCCACCACGGCCCGCATACGGGATACGCTTCGGCGAGTGCTTAACCTACCTCCCAACACCATTATGGAAT
ACAAAACCCACACCGACAGCATCAAA

Alignment

ORF - retro_btau_1498 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 94.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNNKFDALKDDDSGDHDQNEENSTQKDGEKEKTERDKSQSSSKRKAVVPGPAEHPLQYNYTFWYSRRTPG
          MNNKFDALKDDDSGDHDQNEENSTQKDGEKEKTERDKSQSSSKRKAVVPGPAEHPLQYNYTFWYSRRTPG
Retrocopy MNNKFDALKDDDSGDHDQNEENSTQKDGEKEKTERDKSQSSSKRKAVVPGPAEHPLQYNYTFWYSRRTPG

Parental  RPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLR
          RPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLR
Retrocopy RPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLR

Parental  KGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNT
          KGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNT
Retrocopy KGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNT

Parental  IMEYKTHTDSIK
          IMEYKTHTDSIK
Retrocopy IMEYKTHTDSIK

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	0.07 RPM	2.23 RPM
ERP005899_muscle	1.90 RPM	10.08 RPM
SRP017611_brain	0.87 RPM	6.53 RPM
SRP017611_kidney	2.02 RPM	9.25 RPM
SRP017611_liver	0.91 RPM	2.64 RPM
SRP030211_testis	1.38 RPM	17.01 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1498 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1498 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304,
Bos taurus	ENSBTAG00000003103	1 retrocopy	retro_btau_1679,
Bos taurus	ENSBTAG00000009522	3 retrocopies	retro_btau_1094, retro_btau_1702, retro_btau_944,
Bos taurus	ENSBTAG00000010598	2 retrocopies	retro_btau_1232, retro_btau_1498 ,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Mustela putorius furo	ENSMPUG00000005206	2 retrocopies	retro_mputfur_110, retro_mputfur_1554,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,