RetrogeneDB ID: retro_mdom_432

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:512633229..512634727(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3L
• Ensembl ID: ENSMODG00000019068
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit L [Source:HGNC Symbol;Acc:18138]

Sequence

>retro_mdom_432
GCCACCATGTCCTACCCGTCCAAGGATTACGACAACGAGGCTACATGTGATCCCTATGCTTACCCTGGAGACGATGACAT
GCACACAGGAGACCCAAAGCATGAGCAGCAGACCTATCAAGTAATTCCAGAAGTGATCAAGGATTTCATCCACTATTCCC
ATAAAACTGTCTCCGACCTTATCTACCAGAAAGTGTATGAGCTCCAGGCAAGCCGGGTGTCCAACGATGTTATCGACCAA
AAGGTGTATAAGATCCAGGACATCTATGAGAACAGCTGGACCAAGCTGACTGAAAGGTTCTTCAAGAATACTCCCTGGCC
AGAAGCTGAGGCCATTGCCCCACAAGTTGGCAATGATGCTGTCTTCTTGATCCTGTCTAAGGAACTTTATTACAGACCCA
TCTATGCCAATGTCAGCAGTGGGCCTTCCTTGGAACAAAGGTTTGAGTCCGATTACAACTATTGCAACCTTTTCAACTAC
ATTCTCAATGCTGATGGACCTGCCCCCCTTGAACTGCCCAACCAGTGGCTGTGGGATATCATTGATGAATTCATCTAAGA
GTTTCAGTCATTCAATCAATACCAGTGGAAGACGGCTAAAAAGTCACATGAGGAGATTAACTTTCTTCGTTCGAACCCCA
AGGTCTGGAATGTCCACAGCGTCCTCAATGTGCTTCATCCCCTTGTAGACAAATCCAACATCAACTGGCAGCTAGAAGTC
TACCCCAGTGGAGATGACCCTGAGAGTGTGGCTAGTGAATATGGCCGGCACTCCCTCTACAAGATGCTTGGCTACTTCAG
CCTGGTGGGACTGCTCTGGCTGCACTCCCTCTTGGGGGATTACTACCAGGCTATCAAGGTGCTGGAGAACATTGAATTGA
ACAAGAAGAGCATGTATTCCCGGGTGCCTGAATGCCAGGTCACCACCTATTACTATGTGGGGTTTGCCTACTTGATGATG
GGCTGGTACCAGGATGCCAACATTTGTGTCTTTGCCAACATCCTGCTCTACATTCAGAGAACCAAGAGCATGTTTCAGAG
AACAATGTACAAATATGAGATGATCAACAAGCAGAATGAGCAAATGCACGCCCTGCTGGCCATTGTCCTGACCATGTACC
CCATGCACATTGATGAGAGCATTCACCTGCAGCTCTGAGAGAAGTATGGAGACAAGATGCTGCGCATGGCAGAAGGGAGA
CACCCAGGCATATGAGGAGCTCTTTAGCTACTCCTGCCCCAAGTTCCTGTCCCCCATCGTGCCCAACTACGACAACATGC
ACCCCAACTACCACAAGGAGCCCTTCCTGCAACAGCTGAAGGTGTTTCCAGATGAGGTATAGCAGCAGGCCCAGCTGTCC
ACTATTCACAGCTTTCTGAATCTCTATACCACCATGCTTGTGGCCAAGCTGGCTGGTTTCTTGGACTTCACTGAACAGGA
GTTTCGTATCCAGCTGCTGGTCTTCAAACACAAGATGAAGAACCTGATGTGGACATCT

Alignment

ORF - retro_mdom_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 89.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAMSYPSEDYDNEAAYDPYAYPGDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKDFIQYFHKTVSDLID
          A.MSYPS.DYDNEA..DPYAYPGD.DMHTGDPK.....E.Q..Q....VI...I.....Y.HKTVSDLI.
Retrocopy ATMSYPSKDYDNEATCDPYAYPGDDDMHTGDPK----HEQQTYQVIPEVIKDFI----HYSHKTVSDLIY

Parental  QKVYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKELYYR
          QKVYELQASRVS.DVIDQKVY.IQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLIL.KELYYR
Retrocopy QKVYELQASRVSNDVIDQKVYKIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILSKELYYR

Parental  HIYAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRWKTAKKS
          .IYA.VS.GPSLEQRFES.YNYCNLFNYILNADGPAPLELPNQWLWDIIDEFI..FQSF.QY.WKTAKKS
Retrocopy PIYANVSSGPSLEQRFESDYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFI*EFQSFNQYQWKTAKKS

Parental  DEEIDFLRSNPKVWNVHSVLNVLHSLVDKSNINRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLL
          .EEI.FLRSNPKVWNVHSVLNVLH.LVDKSNIN.QLEVY.SG.DPESVA.EYGRHSLYKMLGYFSLVGLL
Retrocopy HEEINFLRSNPKVWNVHSVLNVLHPLVDKSNINWQLEVYPSGDDPESVASEYGRHSLYKMLGYFSLVGLL

Parental  RLHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDA-IRVFANILLYIQRTK
          .LHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMM..YQDA.I.VFANILLYIQRTK
Retrocopy WLHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMGWYQDANICVFANILLYIQRTK

Parental  SMFQRTTYKYEMINKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKMLRM-QKGDPQVYEELFSYS
          SMFQRT.YKYEMINKQNEQMHALLAI.LTMYPM.IDESIHLQL.EKYGDKMLRM.QKGD.Q.YEELFSYS
Retrocopy SMFQRTMYKYEMINKQNEQMHALLAIVLTMYPMHIDESIHLQL*EKYGDKMLRM>QKGDTQAYEELFSYS

Parental  CPKFLSPVVPNYDNMHPNYHKEPFLQQLKVFADEVQQQAQLSTIRSFLKLYTTMPVAKLAGFLDLTEQEF
          CPKFLSP.VPNYDNMHPNYHKEPFLQQLKVF.DEV.QQAQLSTI.SFL.LYTTM.VAKLAGFLD.TEQEF
Retrocopy CPKFLSPIVPNYDNMHPNYHKEPFLQQLKVFPDEV*QQAQLSTIHSFLNLYTTMLVAKLAGFLDFTEQEF

Parental  RIQLLVFKHKMKNLVWTS
          RIQLLVFKHKMKNL.WTS
Retrocopy RIQLLVFKHKMKNLMWTS

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	0.60 RPM	0.00 RPM
SRP007412_cerebellum	0.65 RPM	0.00 RPM
SRP007412_heart	0.40 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.59 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_432 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_432 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001443	3 retrocopies	retro_cfam_1496, retro_cfam_1877, retro_cfam_315,
Callithrix jacchus	ENSCJAG00000012225	1 retrocopy	retro_cjac_1234,
Cavia porcellus	ENSCPOG00000005885	2 retrocopies	retro_cpor_1288, retro_cpor_410,
Homo sapiens	ENSG00000100129	1 retrocopy	retro_hsap_1369,
Monodelphis domestica	ENSMODG00000019068	3 retrocopies	retro_mdom_1247, retro_mdom_1585, retro_mdom_432 ,
Otolemur garnettii	ENSOGAG00000029444	1 retrocopy	retro_ogar_1635,
Pongo abelii	ENSPPYG00000011806	2 retrocopies	retro_pabe_1135, retro_pabe_1136,
Pan troglodytes	ENSPTRG00000014352	1 retrocopy	retro_ptro_940,
Pteropus vampyrus	ENSPVAG00000010103	1 retrocopy	retro_pvam_648,
Rattus norvegicus	ENSRNOG00000011020	1 retrocopy	retro_rnor_2122,