RetrogeneDB ID: retro_cpor_1146

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_5:671862..672738(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S1
• Ensembl ID: ENSCPOG00000003313
• Aliases: None
• Description: None

Sequence

>retro_cpor_1146
GTGCCAGGTCTAAATTATAGATTTTATTAACACAAATTTCCTGAGGTGGAAGATGTAGTGATAGTAGATGTACGGTCCAT
AACTGAAATGGGGGCTAATGTCAGTTTGCTGGAATACAACATCAAAGGCATGATTCTTCCTAGTGAATTATCCAGGAGAG
GTATCGGTTCTATAAACAAACTCATTTGAATAGGCAGGAATGAATGTGTGGCTGTCATTAGCGGGGACAAAGAAAAAAGG
ATACATTGATTTGTCAAAAATAAGTTTCTCTAGAGGAAGTAATCAAATGTGAGGACAATTTCACAAAATCCAAAACTGTT
TATAGCATTCTTTGCCATGTTGTTGAGGTGTTACAATATATCAAGGATGAACAGCTGGAAAGCCCACTCCAGAGGACTTC
CTGGGTCTTTGATGCAAGTACAAGAGACCTGGTTATGGTGTCTATGATGCATTTAAGCATGCAGTCTCAGATTCCTAAAT
TTTGGATAGATTAGATTTGAATGACAATGAACGGAGGTCCTCATTAATATTATTAATATTGACCCCACAAGCTGTCAAAA
GTTGAGTGGACACTGAAGTAGCTTGTTATGGTTATGAAGGCATCAATGCTGTGAAAGAAGCCCTGAGAGCAGGTTTGAAT
TGTTCAACAGAGACCATGCCATCAAGATCAATCTAGTAGCTCCTCCTCGGTATGTGATGACTACAGCAACCCTGAGAGAG
CAGAAGGTCTCAGTTCTCAGTCAAGCCATGGCTGTTATCAAAGAAAAGAGTGAAGAAAAGAGGGCTCTTTTCAGTGTTCA
GATGGGTCCCAAAGTGGTCACAGATACAGACGAGGCTGAGCTCATGAGGCAGCTGGAGAGGTTTGAGACAGAAAAC

Alignment

ORF - retro_cpor_1146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 94.29 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNEC
          .PGL..RFY.HKFPEVEDVV.V.VRSI.EMGA.VSLLEYN.I.GMIL.SELSRR.I.SINKLI.IGRNEC
Retrocopy VPGLNYRFY*HKFPEVEDVVIVDVRSITEMGANVSLLEYN-IKGMILPSELSRRGIGSINKLI*IGRNEC

Parental  VVVIRVDKEKGYIDLSKRR-VSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFD
          V.VI..DKEK......K...VS.EE.IKCED.FTKSKTVYSIL.HV.EVL.Y.KDEQLES..QRT.WVFD
Retrocopy VAVISGDKEKRIH*FVKNK<VSLEEVIKCEDNFTKSKTVYSILCHVVEVLQYIKDEQLESPLQRTSWVFD

Parental  D-KYKRPGYGAYDAFKHAVSDPSILDSLDLNE-DEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDA
          ..KYKRPGYG.YDAFKHAVSD..ILD.LDLN....R..LI..I...LTPQAVK...D.EVACYGYEGI.A
Retrocopy A<KYKRPGYGVYDAFKHAVSDS*ILDRLDLNDNERRSSLILLI---LTPQAVKS*VDTEVACYGYEGINA

Parental  VKEALRAGLNCSTETMP-IKINLIAPPRYVMTTTTLERTEGLSVLNQAMAVIKEKIEEKRGVFNVQMEPK
          VKEALRAGLNCSTETMP.IKINL.APPRYVMTT.TL.R....SVL.QAMAVIKEK.EEKR..F.VQM.PK
Retrocopy VKEALRAGLNCSTETMP<IKINLVAPPRYVMTTATL-REQKVSVLSQAMAVIKEKSEEKRALFSVQMGPK

Parental  VVTDTDETELARQLERLEREN
          VVTDTDE.EL.RQLER.E.EN
Retrocopy VVTDTDEAELMRQLERFETEN

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
SRP017611_brain	0.00 RPM	27.84 RPM
SRP017611_kidney	0.00 RPM	36.22 RPM
SRP017611_liver	0.00 RPM	26.86 RPM
SRP040447_lung	0.03 RPM	27.16 RPM
SRP040447_skeletal_muscle	0.00 RPM	19.17 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1146 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1146 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,