RetrogeneDB ID: retro_cjac_2067

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:20399943..20400883(+)
• Located in intron of: ENSCJAG00000000762

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S1
• Ensembl ID: ENSCJAG00000015368
• Aliases: None
• Description: eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa [Source:HGNC Symbol;Acc:3265]

Sequence

>retro_cjac_2067
ATGCCAGGTCTAAGTTGGAGATTTTATCAACACAAATTTCCTGAGGTAGAAGATGTAGTGATGGTGAATGTAAGATCCAT
TGCTGAAATGGGTGCTTATGTCAGCTTGCTGAAATACAACAACATTGAAGGCATGGTTTTTCTTAGTGAATTATCCAGAA
GGCGTATCCGTTCTATAAACAAACTGATCCAAATTGGCAGGAATGAGTGTGTGGTTGTCATTAGGGTGGACAAAGAAAAA
GGATATATAGATATGTCAAAAAGAAGAGTTTCTCCAGAGGAAGCAATCAAATGTGAAGACAAATTCACAAAATCCAAAAC
TATTTACAGCATTCTTCGTCATGTTGCTGAGGTGTTCAAATACACCAAGGATGAACAGCTGGAAAGCCTATTCCAGACGA
CTGCCTGGGTCGTTGATGACAAGTACAAGAGACCTGGATATGGTGCCTATGATGCATTTAAGCATGCAGTCTGAGACCCG
TCTATTTTGGATAGTTTAGGTTTGAATGAAGATGAATGGGAAGTACTCAATAATATTAATAGGTGCTTGACCCCACAGGC
TGTCAAAATTCCAGCGGATATTGAAGTGGCTTGTTACGGTTATGAAGGCATTGATGCTGTAAAAGAAGCCCTAAGAGCAG
GTTTGAATTGATCTACAGAAACCATGCCCATTAAGATTAATCTAATAGCTCCTCCTCGGTATATAATGACTACCACAACC
CTGGAGAGAAGAGAAGGCCTTTCTGTCCTCAGTCAAGCAATGGCTGTTATCAAAGAAAAGAGTGAGAAAAAGAGGGGTGT
GTTCAATGTTCAAATGGAGCCCAAAGTGATCAGATATAGATGAGACTGAACTTGTGAGACAGATGGAGAGGCTTGAAAGA
GAAAATGCCGAAGTGGATGGAGATGATGATGCAGAAGAAATGGAAGCCAAAGCTGAAGAT

Alignment

ORF - retro_cjac_2067 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNEC
          MPGLS.RFYQHKFPEVEDVVMVNVRSIAEMGAYVSLL.YNNIEGM..LSELSRRRIRSINKLI.IGRNEC
Retrocopy MPGLSWRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLKYNNIEGMVFLSELSRRRIRSINKLIQIGRNEC

Parental  VVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDD
          VVVIRVDKEKGYID.SKRRVSPEEAIKCEDKFTKSKT.YSILRHVAEV..YTKDEQLESLFQ.TAWV.DD
Retrocopy VVVIRVDKEKGYIDMSKRRVSPEEAIKCEDKFTKSKTIYSILRHVAEVFKYTKDEQLESLFQTTAWVVDD

Parental  KYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKE
          KYKRPGYGAYDAFKHAV.DPSILDSL.LNEDE.EVL.NNINR.LTPQAVKI.ADIEVACYGYEGIDAVKE
Retrocopy KYKRPGYGAYDAFKHAV*DPSILDSLGLNEDEWEVL-NNINRCLTPQAVKIPADIEVACYGYEGIDAVKE

Parental  ALRAGLNCSTETMPIKINLIAPPRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQME-PKVVT
          ALRAGLN.STETMPIKINLIAPPRY.MTTTTLER.EGLSVLSQAMAVIKEK.E.KRGVFNVQME.PK...
Retrocopy ALRAGLN*STETMPIKINLIAPPRYIMTTTTLERREGLSVLSQAMAVIKEKSEKKRGVFNVQME>PK*-S

Parental  DTDETELARQMERLERENAEVDGDDDAEEMEAKAED
          D.DETEL.RQMERLERENAEVDGDDDAEEMEAKAED
Retrocopy DIDETELVRQMERLERENAEVDGDDDAEEMEAKAED

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
SRP051959_colon	0.64 RPM	21.94 RPM
SRP051959_heart	0.47 RPM	17.08 RPM
SRP051959_kidney	0.60 RPM	25.94 RPM
SRP051959_liver	0.19 RPM	28.64 RPM
SRP051959_lung	1.24 RPM	20.71 RPM
SRP051959_lymph_node	0.89 RPM	20.36 RPM
SRP051959_skeletal_muscle	0.17 RPM	20.13 RPM
SRP051959_spleen	0.99 RPM	22.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2067 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2067 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2067 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,