RetrogeneDB ID: retro_mdom_1754

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:223904704..223905337(+)
• Located in intron of: ENSMODG00000021206

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S1
• Ensembl ID: ENSMODG00000009911
• Aliases: None
• Description: eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa [Source:HGNC Symbol;Acc:3265]

Sequence

>retro_mdom_1754
TTCACCAACTCCAGAACTGTTTTATGGAACCTTTGCCATGCTGCTGAAGTGTTAGAATACAGAAAAGATGAGCAGCTGCA
GAGCCTGCTCCAGAGAACTGTCTGGGTCTTTGAAGCCAAGTACAAAAGACCAGGTCATGGTGCCTAGGATGCATTTAAAC
ACGCAGTCTCAGACCCTCCAGTCCCAGGTGGACTGGATTTGAATGAAGATGAAAGGCAAATACTGATTGATAACATAAAT
AGGAGCTTGACACTATAAGCTGTCAAAATCCAAGTTGTATTGAAGTGACTTATAATTATGAGGATATTGATGCTGTGAAA
GAAGCTCTTAAAGCAGTTTGAATTGCTGCACAGAAAACATGCCTATAAAGATTAACCTGAAAGCACCTTCTTGATAGCTG
ATCACTTCAACAATCTTAGACAGAACAGAAGGTCTTTCTGTCCTCAATCAGACTAGACTGTCATCAAAGAAAAGACTGAG
AAGAGGGTTGTCTTCTACGTTCAAATGGAGCCCAAACATGTCACAGACACATATGAAACTGATCTTGGAAGACAACTGGA
GAGGCTTGAATGGGAAAATGCTGAGGTGGAGGGATGTGATGATTCTGAAGAAATGGAAGCCAACACTGAAGAT

Alignment

ORF - retro_mdom_1754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 67.94 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FTKSKTVYSILRHVAEVLEYSKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDGLDLNED
          FT.S.TV...L.H.AEVLEY.KDEQL.SL.QRT.WVF..KYKRPG.GA.DAFKHAVSDP....GLDLNED
Retrocopy FTNSRTVLWNLCHAAEVLEYRKDEQLQSLLQRTVWVFEAKYKRPGHGA*DAFKHAVSDPPVPGGLDLNED

Parental  ERRVLIDNINRRLTPQAVKIR-ADIEVACYGYEGIDAVKEALRA-GLNCSTENMPIKINLIAPPRYVMTT
          ER..LIDNINR.LT..AVKI....IEV..Y.YE.IDAVKEAL.A..LNC.TENMPIKINL.AP.....T.
Retrocopy ERQILIDNINRSLTL*AVKIQ<SCIEVT-YNYEDIDAVKEALKA<SLNCCTENMPIKINLKAPS**LITS

Parental  TTLERTEGLSVLNQAM-AVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQLERLERENAEVDGDDDAEE
          T.L.RTEGLSVLNQ....VIKEK..EKR.VF.VQMEPK.VTDT.ET.L.RQLERLE.ENAEV.G.DD.EE
Retrocopy TILDRTEGLSVLNQTR<TVIKEK-TEKRVVFYVQMEPKHVTDTYETDLGRQLERLEWENAEVEGCDDSEE

Parental  MEAKAED
          MEA..ED
Retrocopy MEANTED

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
SRP007412_brain	0.00 RPM	107.04 RPM
SRP007412_cerebellum	0.00 RPM	93.69 RPM
SRP007412_heart	0.00 RPM	113.23 RPM
SRP007412_kidney	0.00 RPM	190.94 RPM
SRP007412_liver	0.00 RPM	136.45 RPM
SRP007412_testis	0.00 RPM	605.80 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1754 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1754 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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,