RetrogeneDB ID: retro_rnor_2218

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:69458909..69459777(-)
• Located in intron of: ENSRNOG00000005723

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif2s1
• Ensembl ID: ENSRNOG00000009432
• Aliases: None
• Description: Eukaryotic translation initiation factor 2 subunit 1 [Source:UniProtKB/Swiss-Prot;Acc:P68101]

Sequence

>retro_rnor_2218
GTTGCTGAGATGGGGCCCTATGTCAGCTTGTTGGAATCTAATAACTTTGAAGGCATGATTCTTCTTAGTGAGTTATCCAG
ACAACGTATTCATTCCACAAACAAACTGATCAGAATTGGCAGAAATGAGTGTGTAGTTGTCATTAGAATGGATAAAGAAA
AGGGATATATAGATTTGTCAAAAAGAAGAGTTTCTCCAGAGGAAGCAATCAAGTGTGAAAACAAATTCGCAAGATCCAAA
ACTGTTTCTAGCATTCTTCGCCATGTTGCTGGGGTATTAGAATATACCAAGGATGAGCAGCTGGAAAGCCTATTCCAGTG
GACTGCCTGAGTCTTCGATGACAAGTACAAGAGACCTGGATATGGTGCCTATGATGCCTTTAAGCACGCAGTCTCAATCC
CATCTATCTTGGATAGTTTAGATTTGAATGAAGATGAAAGGGAAGTCCTCATTAACAATATCAAATAGGCATTTGACCCC
ACAAGCTGTCAAAATTTGAGCAGCTATTGAAGTAGCTTGCTATGGTTATGAAGGCAGTAATGTTGTAAAAGGATTCCTAG
GGGCAGGTTTGACTTGTTCTACAGAAACCACGCCCTTCAAGCTTAATCTAATAGCTCCACCCAGGTATGAGATAATAACA
ACGGCCCTAGAGAGGACAGGACGACTCTCTGTCCTCAGTCAGGCTATAGCAGTTATCAAAGAGAAGATTGAGGAGAAGAA
GGGAGTGGGCAATGTTCAGATGGAGTCCAAAGTGGTCACAGATACAGATGAGAGTGAACATGCAAGGCAGCTGGAATGGC
TTGAGAGAGAAAATGCAGAAGTGGATGGAGATGATGATGCAGAAGAAATGGAAGCCAAAGCTGAAGAT

Alignment

ORF - retro_rnor_2218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.83 %
• Parental protein coverage: 91.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAI
          .AEMG.YVSLLE.NN.EGMILLSELSR.RI.S.NKLIRIGRNECVVVIR.DKEKGYIDLSKRRVSPEEAI
Retrocopy VAEMGPYVSLLESNNFEGMILLSELSRQRIHSTNKLIRIGRNECVVVIRMDKEKGYIDLSKRRVSPEEAI

Parental  KCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSL
          KCE.KF..SKTV.SILRHVA.VLEYTKDEQLESLFQ.TA.VFDDKYKRPGYGAYDAFKHAVS.PSILDSL
Retrocopy KCENKFARSKTVSSILRHVAGVLEYTKDEQLESLFQWTA*VFDDKYKRPGYGAYDAFKHAVSIPSILDSL

Parental  DLNEDEREVLINNI-NRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTETMPIKINLIAPPRY
          DLNEDEREVLINNI.NR.LTPQAVKI.A.IEVACYGYEG...VK..L.AGL.CSTET.P.K.NLIAPPRY
Retrocopy DLNEDEREVLINNI>NRHLTPQAVKI*AAIEVACYGYEGSNVVKGFLGAGLTCSTETTPFKLNLIAPPRY

Parental  VMTTTTLERTEGLSVLNQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQLERLERENAEVDGDDD
          ...TT.LERT..LSVL.QA.AVIKEKIEEK.GV.NVQME.KVVTDTDE.E.ARQLE.LERENAEVDGDDD
Retrocopy EIITTALERTGRLSVLSQAIAVIKEKIEEKKGVGNVQMESKVVTDTDESEHARQLEWLERENAEVDGDDD

Parental  AEEMEAKAED
          AEEMEAKAED
Retrocopy AEEMEAKAED

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	27.75 RPM
SRP017611_kidney	0.00 RPM	31.89 RPM
SRP017611_liver	0.00 RPM	19.36 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2218 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2218 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,