RetrogeneDB ID: retro_mmus_1927

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:66942558..66943050(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082218
• 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_1927
GCCTTTAAGCATGCAGTCTCAGACCCATCTATCTTGGATAGTTTAGATTTGAATGAAGATGAAAGAGAAGTACTCATTAA
CAATATCAATAGGCATTTGACCCCACAAGTAGTCAAAATTCAAACAGATATTGAAGTAGCTTGCTATGGTTATGAAGGCA
TTGATGCTGTAAAAGAAGCCCCGAGGGCAGGTTTGAATTGTTCTACAGAAACCATGCCCATCAAGATTAATCTAATAGTT
CCACACAGGTATGTGATGACAACAACGACCCTAGAGAAGACAGAAGGCCTCTCTGTCCTCAATCAGGCTATGGCAGTCAT
CAAAGAGAAGATCTAGGAGAAGAGGGGAGTTTTCAATGTTCAGATGGAGCCCAAAGTGGTCACAGATACAGATGAGACTG
AACTTGCAAGACAGCTAGAATGGCTTGAGAGAGAAGATGCAGAAGTGGATGGAGACAACAATGCAGAAGAAATGGAAGCC
AAAGCTGAAGAT

Alignment

ORF - retro_mmus_1927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.07 %
• Parental protein coverage: 52.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTE
          AFKHAVSDPSILDSLDLNEDEREVLINNINR.LTPQ.VKI..DIEVACYGYEGIDAVKEA.RAGLNCSTE
Retrocopy AFKHAVSDPSILDSLDLNEDEREVLINNINRHLTPQVVKIQTDIEVACYGYEGIDAVKEAPRAGLNCSTE

Parental  TMPIKINLIAPPRYVMTTTTLERTEGLSVLNQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQLE
          TMPIKINLI.P.RYVMTTTTLE.TEGLSVLNQAMAVIKEKI.EKRGVFNVQMEPKVVTDTDETELARQLE
Retrocopy TMPIKINLIVPHRYVMTTTTLEKTEGLSVLNQAMAVIKEKI*EKRGVFNVQMEPKVVTDTDETELARQLE

Parental  RLERENAEVDGDDDAEEMEAKAED
          .LERE.AEVDGD..AEEMEAKAED
Retrocopy WLEREDAEVDGDNNAEEMEAKAED

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	0.04 RPM	20.41 RPM
SRP007412_heart	0.00 RPM	26.24 RPM
SRP007412_kidney	0.00 RPM	28.24 RPM
SRP007412_liver	0.03 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_1927 was not detected

EST

No EST(s) were mapped for retro_mmus_1927 retrocopy.

TSS

No TSS is located nearby retro_mmus_1927 retrocopy 5' end.

Lab

retro_mmus_1927 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1927 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,