RetrogeneDB ID: retro_rnor_1234

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:57565357..57566018(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000022401
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1234
ATGCCAGGTCTAAGCTGTAGATTTTATCAACCCAAATTTCCTGAGGTGGAAGATGTAGTGATGGTGATTGTAAGATCCAT
TGCTGAAATGGGGGCCTATGTCAGCTTGTTGGAATATAACAACATTGAAGGCATGATTCTTCTTAGTGAATTATCTAGAC
GACGTATCCGTTCTATAACCAAACTGATCCAAATTGGCAGAAATGAATTGTGTAATTGTCATTAGAGTGGATAAAGAAAA
AGGATACATAGATTTGTCGAAAAGAAGAGTTTCTCCAGAGGAAGCAATCAAATGTGAAGACAAATTCATAAAATTCAAAA
CTGTTGATAGCATTCTTCGCCATGTTGCTGAGGTATTAGAGTATACCAAGGATGAGCAGCTGGAAAGCCTATTCCAGAGG
ACTGCCTGGGTCATTGATGACAAGTGCAAGAGACCTGGGTATGGTGCCTATGATGCCTTTAAGCATGCAGTCTCAGACCC
ATCTATCTTGGATGGTTTAGATTTGAATGAAGATGAAAGAGAAGTCCTCGTTAACAATATCAACAGGCGTTTGACCCCAC
AAGCTGTCAAGATTCGAGCAGATATTGAAGAAGCTTGCTATGAATGCATTGATGCTGTAAAAGAAGCCCTAAGAGCAGGT
TTGAATTATTCTACAGAAACC

Alignment

ORF - retro_rnor_1234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.93 %
• Parental protein coverage: 70.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNE-
          MPGLSCRFYQ.KFPEVEDVVMV.VRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSI.KLI.IGRNE.
Retrocopy MPGLSCRFYQPKFPEVEDVVMVIVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSITKLIQIGRNE>

Parental  CVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFD
          CV.VIRVDKEKGYIDLSKRRVSPEEAIKCEDKF.K.KTV.SILRHVAEVLEYTKDEQLESLFQRTAWV.D
Retrocopy CVIVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFIKFKTVDSILRHVAEVLEYTKDEQLESLFQRTAWVID

Parental  DKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVK
          DK.KRPGYGAYDAFKHAVSDPSILD.LDLNEDEREVL.NNINRRLTPQAVKIRADIE.AC..YE.IDAVK
Retrocopy DKCKRPGYGAYDAFKHAVSDPSILDGLDLNEDEREVLVNNINRRLTPQAVKIRADIEEAC--YECIDAVK

Parental  EALRAGLNCSTET
          EALRAGLN.STET
Retrocopy EALRAGLNYSTET

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_1234 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1234 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1234 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,