RetrogeneDB ID: retro_btau_1191

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:19477925..19478870(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S1
• Ensembl ID: ENSBTAG00000016311
• Aliases: None
• Description: Eukaryotic translation initiation factor 2 subunit 1 [Source:UniProtKB/Swiss-Prot;Acc:P68102]

Sequence

>retro_btau_1191
ATGCCGGGTCTAAGTTGTAGATTTTATCAACACAAATTTCCTGAGGTGGAAGATGTAGTGATGGTGAATGTAAGGTCCAT
TGCTGAAATGGGCGCTTATGTCAGCTTGCTGGAATACAACAACATCGAAGGCATGATTCTTCTGAGTGAGTTGTCAAGAA
GGTGTATCCGTTCTATAAACAAACTCATCCGAATTGGCAGGAATGAATGTGTGGTTGTTATTAGAGTGGACAAAGAAAAA
GGATATATTGATTTGTCAAAAAGAAGAGTTTCACCAGAGGAAGCAATCAAATGTGAAGATAAATTTACCAAATCCAAAAC
TGTTTACAGCATTCTTCGTCATGTTGCTGAGGTCTTAGAATATACCAAGGATGAGCAGCTGGAAAGCCTATTCCAGAGGA
CTGCCTGGGTCTTCGATGACAAGTACAAGAGACCCGGATATGGTGCCTATGATGCATTTAAGCACGCAGTCTCAGACCCA
TCTATTTTGGATAGCTTAGATTTGAATGAAGATGAACGTGAAGTACTCATTAACAATATTAATAGGCGTTTGACCCCCCA
GGCTGTCAAAATTTGAGCAGATATTGAAGTGGCTTGTTATGGTTATGAAGGCATCGATGCCGTAAAAGAAGCTCTGAGAG
CGGGTTTGAATTGTTCTACAGAAACCATGCCCATCAAAATTAATCTAATAGCTCCTCCTCGGTATGTAATGACTACAACC
ACCCTGGAGAGAACAGAAGGCCTCTCTGTCCTCAATCAAGCTATGGCTGTTATAAAAGAAAAAATTGAGGAAAAGAGGGG
TGTCTTCAATGTTCAAATGGAGCCCAAAGTGGTCACAGATACAGATGAGACCGAACTTGCAAGGCAGCTGGAGAGGCTTG
AGAGAGAAAATGCAGAAGTGGATGGAGATGATGATGCAGAAGAAATGGAAGCCAAAGCTGAAGAT

Alignment

ORF - retro_btau_1191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNEC
          MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRR.IRSINKLIRIGRNEC
Retrocopy MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRCIRSINKLIRIGRNEC

Parental  VVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDD
          VVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDD
Retrocopy VVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDD

Parental  KYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKE
          KYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKI.ADIEVACYGYEGIDAVKE
Retrocopy KYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKI*ADIEVACYGYEGIDAVKE

Parental  ALRAGLNCSTETMPIKINLIAPPRYVMTTTTLERTEGLSVLNQAMAVIKEKIEEKRGVFNVQMEPKVVTD
          ALRAGLNCSTETMPIKINLIAPPRYVMTTTTLERTEGLSVLNQAMAVIKEKIEEKRGVFNVQMEPKVVTD
Retrocopy ALRAGLNCSTETMPIKINLIAPPRYVMTTTTLERTEGLSVLNQAMAVIKEKIEEKRGVFNVQMEPKVVTD

Parental  TDETELARQLERLERENAEVDGDDDAEEMEAKAED
          TDETELARQLERLERENAEVDGDDDAEEMEAKAED
Retrocopy TDETELARQLERLERENAEVDGDDDAEEMEAKAED

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	4.18 RPM
ERP005899_muscle	0.11 RPM	17.16 RPM
SRP017611_brain	0.41 RPM	7.40 RPM
SRP017611_kidney	0.12 RPM	9.25 RPM
SRP017611_liver	0.23 RPM	6.87 RPM
SRP030211_testis	0.98 RPM	28.29 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1191 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1191 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1191 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016311	1 retrocopy	retro_btau_1191 ,
Callithrix jacchus	ENSCJAG00000015368	1 retrocopy	retro_cjac_2067,
Cavia porcellus	ENSCPOG00000003313	1 retrocopy	retro_cpor_1146,
Echinops telfairi	ENSETEG00000019003	1 retrocopy	retro_etel_279,
Monodelphis domestica	ENSMODG00000009911	1 retrocopy	retro_mdom_1754,
Mus musculus	ENSMUSG00000021116	4 retrocopies	retro_mmus_1342, retro_mmus_1927, retro_mmus_1960, retro_mmus_728,
Oryctolagus cuniculus	ENSOCUG00000012023	1 retrocopy	retro_ocun_1677,
Rattus norvegicus	ENSRNOG00000009432	3 retrocopies	retro_rnor_1234, retro_rnor_1423, retro_rnor_2218,
Sarcophilus harrisii	ENSSHAG00000009815	1 retrocopy	retro_shar_560,