RetrogeneDB ID: retro_mmus_1960

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:108572893..108573528(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082113
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eif2s1
• Ensembl ID: ENSMUSG00000021116
• Aliases: Eif2s1, 0910001O23Rik, 2410026C18Rik, 35kDa, Eif2a, eIF2alpha
• Description: eukaryotic translation initiation factor 2, subunit 1 alpha [Source:MGI Symbol;Acc:MGI:95299]

Sequence

>retro_mmus_1960
TCACGAAATCCAAAACTGTTTAGCATTCTTTACCATGTTGCTGAGGTATTAGAATATACTAAGAATGAGCAGCTGGAAAG
CCTGGTCCAGAGGACTGTCTTGCTCTTTGATGGCAAGTACCAGGGACCTGGATATGGTGCCTATGATGCCTTTAAGCATG
CAATCTCAGACCCATCTATCTTGGATAGTTTAGATTTGAATGAAGATGAAAGAGAAGTACTCATTAACAATATCAATAGG
CATTCGACCCCACAAGCGGTCAAAATTCGAGCAGATATTAAAGTAGCTTGCTATGGTTATATAGGCATTGATGCTGTAAA
AGAAGCCCTGAGGGCAGGTTTGAATTGTTCTACTGAAACCATGCCTATCAAGATTAATCTAATAGCTCTGCCCAGGTATG
TGATGACAACAAGGACACTAGAGGGGACAGAAGGCCTCTCTGTCCTCAATCAGGCTATGGCAGTCATCAAAGAGAAGATT
GAGAAGAGGAGAGTGTTCAGTGTTTCCATGGAGACAAAGTGGTCACAGATACAGATGAGACTGAACTTGCAAGACAGCTG
GAACGGCTTGAGAGAGAAGATGCAGAAGTGGATGGAGATGATGTTACAGAAGAAATGGAAGCCAAAGCTGAAGAT

Alignment

ORF - retro_mmus_1960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.58 %
• Parental protein coverage: 67.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDE
          .......SIL.HVAEVLEYTK.EQLESL.QRT...FD.KY..PGYGAYDAFKHA.SDPSILDSLDLNEDE
Retrocopy SRNPKLFSILYHVAEVLEYTKNEQLESLVQRTVLLFDGKYQGPGYGAYDAFKHAISDPSILDSLDLNEDE

Parental  REVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTETMPIKINLIAPPRYVMTTTTL
          REVLINNINR..TPQAVKIRADI.VACYGY.GIDAVKEALRAGLNCSTETMPIKINLIA.PRYVMTT.TL
Retrocopy REVLINNINRHSTPQAVKIRADIKVACYGYIGIDAVKEALRAGLNCSTETMPIKINLIALPRYVMTTRTL

Parental  ERTEGLSVLNQAMAVIKEKIEEKRGVFNVQME-PKVVTDTDETELARQLERLERENAEVDGDDDAEEMEA
          E.TEGLSVLNQAMAVIKEKI.EKR.VF.V.ME..KVVTDTDETELARQLERLERE.AEVDGDD..EEMEA
Retrocopy EGTEGLSVLNQAMAVIKEKI-EKRRVFSVSME<DKVVTDTDETELARQLERLEREDAEVDGDDVTEEMEA

Parental  KAED
          KAED
Retrocopy KAED

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
SRP007412_brain	0.00 RPM	25.30 RPM
SRP007412_cerebellum	0.00 RPM	20.41 RPM
SRP007412_heart	0.00 RPM	26.24 RPM
SRP007412_kidney	0.00 RPM	28.24 RPM
SRP007412_liver	0.00 RPM	28.56 RPM
SRP007412_testis	0.00 RPM	106.43 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1960 was not detected

EST

No EST(s) were mapped for retro_mmus_1960 retrocopy.

TSS

No TSS is located nearby retro_mmus_1960 retrocopy 5' end.

Lab

retro_mmus_1960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1960 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,