RetrogeneDB ID: retro_mdom_618

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:550302039..550302920(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2A
• Ensembl ID: ENSMODG00000028858
• Aliases: None
• Description: eukaryotic translation initiation factor 2A, 65kDa [Source:HGNC Symbol;Acc:3254]

Sequence

>retro_mdom_618
GAAAATAGCCCCATCTATGATGTAGTCTGGAATTTCAGTTCCACTGAATTTTGTGCTATTTATGGTTTCATACCTGGCAA
TGCCACAATTTTCTATTTGAAATATGATTTTGTGTTTAACTTTGGTACTGCTTCTCAAAATGGAGACTACTACAGCCTGC
ACAGACATATATTAGTACTTTCTGGGTTTGTAAATCTCAGGGGATAGATGGAAGTGTGGGATGTTAAAACTACAAACTTA
TTTCCAAACCAGTGGCTTCAGATTCATTGTACTTTGTCTGGTGTCCAGATGGAGAACATATTGTAACTGCTACATGTGCT
CCAAGGGTACGTGTTAGTAATGGATACAAGATTTGGCATTACACTGGCTCAATTCTACACAAGTATGATGTCCCATCAAA
TGGAGAAATATAACAAGTGTCTTGGCAGGCAATTTTAGATGGAATATTTCCAGCAAAAGCAGTAACTTACCAAGTACTAC
CAAGTGAAGTGCCAGAGAAGAAGCCTAAGGTTGCAGAAGCTTACAGACCACCAGCCTTAAGTAATAAACCTATAACTAGT
TCCAAACTGCATGAGGGGGAGCCACTACAGAATATGAAACATTCAGGAAATGACAAGTCATTATCTAAAACAGCTCTTAA
AAATCAGAGAAAGCATGAGGCAAAGAAAGCTGCAAAACAGAAGGCAAGAAGTGAAAGTGGTCAAGATTTGATCCATAACT
CAGCTCAGCAATAGAGCATTCCACTAAATGTTGTCTCTCTGCCAACAACAGGAGACCCAGACATAGAAAAAAAAAAGATC
AAGAACCTGAAAAAGAAACTGAAAGCATTTGAACAACTGGAAAAACAAGCAGCTGGTGGTAAACAGATGGAGAAGATCCA
G

Alignment

ORF - retro_mdom_618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.36 %
• Parental protein coverage: 50.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KNGPIYDVVWNSSSTEFCAVYGFMPAKATIFNLKCDPVFDFGTGPRNAAYYSPHGHILVLAGFGNLRGQM
          .N.PIYDVVWN.SSTEFCA.YGF.P..ATIF.LK.D.VF.FGT...N..YYS.H.HILVL.GF.NLRG.M
Retrocopy ENSPIYDVVWNFSSTEFCAIYGFIPGNATIFYLKYDFVFNFGTASQNGDYYSLHRHILVLSGFVNLRG*M

Parental  EVWDVK-NYKLISKPVASDSTYFAWCPDGEHIVTATCAPRLRVSNGYKIWHYTGSILHKYDVPSNAEIWQ
          EVWDVK.NYKLISKPVASDS.YF.WCPDGEHIVTATCAPR.RVSNGYKIWHYTGSILHKYDVPSN.EI.Q
Retrocopy EVWDVK<NYKLISKPVASDSLYFVWCPDGEHIVTATCAPRVRVSNGYKIWHYTGSILHKYDVPSNGEI*Q

Parental  VSWQPFLDGVFPAKAVTYQAVPSEVPEKEPKVAEAYRPPALRNKPITSSKLHEEEPPQNMKHSGNDKPLS
          VSWQ..LDG.FPAKAVTYQ..PSEVPEK.PKVAEAYRPPAL.NKPITSSKLHE.EP.QNMKHSGNDK.LS
Retrocopy VSWQAILDGIFPAKAVTYQVLPSEVPEKKPKVAEAYRPPALSNKPITSSKLHEGEPLQNMKHSGNDKSLS

Parental  KTALKNQRKHEAKKAAKQEARSESGQDLALNSAQQQSTPRNVVSLPTTGDPEV-DKKIKNLKKKLKAIEQ
          KTALKNQRKHEAKKAAKQ.ARSESGQDL..NSAQQ.S.P.NVVSLPTTGDP......IKNLKKKLKA.EQ
Retrocopy KTALKNQRKHEAKKAAKQKARSESGQDLIHNSAQQ*SIPLNVVSLPTTGDPDIXXXXIKNLKKKLKAFEQ

Parental  LKEQAAGGKLLEKNQ
          L..QAAGGK..EK.Q
Retrocopy LEKQAAGGKQMEKIQ

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_618 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_618 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000028858	1 retrocopy	retro_mdom_618 ,
Oryctolagus cuniculus	ENSOCUG00000016095	3 retrocopies	retro_ocun_1771, retro_ocun_1825, retro_ocun_1861,