RetrogeneDB ID: retro_shar_560

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849909.1:2917999..2918874(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S1
• Ensembl ID: ENSSHAG00000009815
• Aliases: None
• Description: eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa [Source:HGNC Symbol;Acc:3265]

Sequence

>retro_shar_560
ATGGTAAATGTATGACCCATTGTTGAGATGGGAGTATATGGAAGTCTATTGGAACACAGCAATATTGAGGGCATGATTCT
TCTTAGTGACTGCCTAGAAGACATATCCACTCCCTCACCAAGCTCATATGAATTGGCAGAAACAAATGTGTGACATGCTT
TAGAGTGGGCAAAGGAAAAGGATTCATTGATTTGTCAAAGATAAGTTTCTCCAGAAGATGCCATCATCTATGAAAACAAA
TTCACCAAATACAAAACTGTTTCTAGCATCCTTCACCATGTTGTTCAGCTGTTAGAGAAGAGTAAGGATGAACAGTTGGA
GAGTCTGTACCAGAGAACTACCTCAGTCATTCTTCACAAGGGTAAGAGGCCAGGATGTAGTGCCTATGATGTATTTAAAC
ATGTAGTCTCAGACCCTTAAGTCCCACATGCACTGAATTTGAATGAAGATGAAGAGAGAGTCCTGATGGATAATATAAAT
AGGGACTTGACATCATAAGCTGTCAAAATTTGAGCTGTTATTGAAGGGGCTTGCTGTGATGATACTGATGCTGTAAAAGA
AGTTCTGAGATTAAGTCTGAGTTGTTCCACAGAAAACATGCCCATCAAAATTAACCTGATAGCACTTCCATGATATGTGA
TGACTACTACAACCTAGAGAGAACAAAAGACCTGTTTTTTCCCTAAAACAAGATATGGCTGTCATAAAAAAAAGATTTAG
GAAAACAGAGGTGTCTCAGTGTTCTGACAGAGTCCAATGTGGTCACTGACACAGATGAAAGTGAGTTTGTAAGGCAACTG
GAGAAGCTTGAGAGGGAAAACACTGAGGCAGATGGATATAATGATGCTGAGGAAATGTAAGCCATAGGGAAAGAT

Alignment

ORF - retro_shar_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.67 %
• Parental protein coverage: 93.65 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MVNVRSIAEMGAYVSLLEYNNIEGMILLSE-LSRRRIRSINKLIRIGRNECVVVIRVDK-EKGYIDLSKR
          MVNV..I.EMG.Y.SLLE..NIEGMILLS..L.RR.I.S..KLI.IGRN.CV...RV.K.EK.......R
Retrocopy MVNV*PIVEMGVYGSLLEHSNIEGMILLSD<LPRRHIHSLTKLI*IGRNKCVTCFRVGK>EKDSL-ICQR

Parental  RVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYSKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVS
          .VSPE.AI..E.KFTK.KTV.SIL.HV...LE.SKDEQLESL.QRT..V...K.KRPG..AYD.FKH.VS
Retrocopy *VSPEDAIIYENKFTKYKTVSSILHHVVQLLEKSKDEQLESLYQRTTSVILHKGKRPGCSAYDVFKHVVS

Parental  DPSILDGLDLNEDERRVLIDNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKIN
          DP.....L.LNEDE.RVL.DNINR.LT..AVKI.A.IE.AC......DAVKE.LR..L.CSTENMPIKIN
Retrocopy DP*VPHALNLNEDEERVLMDNINRDLTS*AVKI*AVIEGACC--DDTDAVKEVLRLSLSCSTENMPIKIN

Parental  LIAPPRYVMTTTT-LERTEGLSVLNQAMAVIKEKIE-EKRGV-FNVQMEPKVVTDTDETELARQLERLER
          LIA.P.YVMTTTT..E.......L.Q.MAV.......E.RGV...V..E..VVTDTDE.E..RQLE.LER
Retrocopy LIALP*YVMTTTT>RENKRPVFSLKQDMAVXXXXFR<ENRGV<LSVLTESNVVTDTDESEFVRQLEKLER

Parental  ENAEVDGDDDAEEMEAKAED
          EN.E.DG..DAEEM.A...D
Retrocopy ENTEADGYNDAEEM*AIGKD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_560 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 ,