RetrogeneDB ID: retro_mdom_1585

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:51513448..51514534(+)
• Located in intron of: ENSMODG00000025137

Retrocopy information

• Ensembl ID: ENSMODG00000004687
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1585
GCCATGTCCTACCTGTCCAAGGATTTCGACGAGGCTGCATATGATCCCTATGCTTACCCTGGCAACTATGACATGCACAC
AGGAGACCCAAAGCAGGACCTAGCCTATGAACAACAATATGAGCAGGAGACCTATCAAGTAATTCCAGACGTGATCAAGG
ATTTCATCCAATATTTCCATAAAACCGTCTCCAACCTTATCGACCAGAAAGTGTATGAGCTCCAGGCAAGCCGGGTGTCC
AGCGACGTTATCAACCAAAAGGTGTATGAGATCCAGGGCATCTATGAGAACAGCTGGACCAAGCTGACTGAAAGGTTCTT
CAAGAATACCCCCTGGCCAGAAGCAGAGGCCATTGCCCCACAAGTTGGCAACGATGCTGTCTTCTTGATCCTGTATAAGG
AACGTTATTACAGAAACATCTATGCCAAAGTCAGCAGCGGGTCTTCCTTGGAACAGAGGTTTGAGTCCTATTACAACTAC
TGCAACCTTTTCAACTACATTCTCAATGCTGATGGACCTGTCCCCCTTGAACTGCCCAACCAGTGGCTGTGGGATATCAT
TGATGAATTCATCTACCAGTTTCAGTCATTCAGTCAATACTGGTGGAAGACGGCTAAAAAGTCAGATGAGGAGATTGACT
TTCTTTATTCCAACCCCAAGGTCTGGAATGTCCACAGCATCCTCAAAGTGCTTCATTCCCTTGTAGACAAATCCAACATC
AACCGGCAGCTAGAAGTCTACACCAGTGGAGGTAACCCTGAGAGTGTGGCTGGTGAGTATGGCCAGCACTCCCTTTACAA
GATGCTTGGCTACTTCATCCTGGTGGGGCTGCTCTGGCTCCACTCCCTCTTGGGGATTACTACCAGGCTATCAAGGTGCT
GGAGAACATTGAGTTGAACAAGAAGAGCATATATTTCCAGGTGCCTGAATGCCAGGTCACCACCTATTACTATGTGGGGT
TTGCCTACTTGATGATACTCCGGTACCAGGAGTTTTTTTTTTTTTTTTGCCAACATCCTGCTCAGCATGTTTCAAAGAAC
AAAATACAAATATGAGATGATCAACAAGCAGAATGAGCAAATGCAC

Alignment

ORF - retro_mdom_1585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.48 %
• Parental protein coverage: 63.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AMSYPSEDYDNEAAYDPYAYPGDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKDFIQYFHKTVSDLIDQ
          AMSY.S.D.D.EAAYDPYAYPG.YDMHTGDPKQDLAYE.QYEQ.TYQVIP.VIKDFIQYFHKTVS.LIDQ
Retrocopy AMSYLSKDFD-EAAYDPYAYPGNYDMHTGDPKQDLAYEQQYEQETYQVIPDVIKDFIQYFHKTVSNLIDQ

Parental  KVYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKELYYRH
          KVYELQASRVSSDVI.QKVYEIQ.IYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKE.YYR.
Retrocopy KVYELQASRVSSDVINQKVYEIQGIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKERYYRN

Parental  IYAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRWKTAKKSD
          IYAKVS.G.SLEQRFESYYNYCNLFNYILNADGP.PLELPNQWLWDIIDEFIYQFQSFSQY.WKTAKKSD
Retrocopy IYAKVSSGSSLEQRFESYYNYCNLFNYILNADGPVPLELPNQWLWDIIDEFIYQFQSFSQYWWKTAKKSD

Parental  EEIDFLRSNPKVWNVHSVLNVLHSLVDKSNINRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLLR
          EEIDFL.SNPKVWNVHS.L.VLHSLVDKSNINRQLEVYTSGG.PESVAGEYG.HSLYKMLGYF.LVGLL.
Retrocopy EEIDFLYSNPKVWNVHSILKVLHSLVDKSNINRQLEVYTSGGNPESVAGEYGQHSLYKMLGYFILVGLLW

Parental  LHSL-LGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQD-AIRVFANILL-YIQRT
          LHSL.LGDYYQAIKVLENIELNKKS.Y..VPECQVTTYYYVGFAYLM..RYQ.......ANILL...QRT
Retrocopy LHSL<LGDYYQAIKVLENIELNKKSIYFQVPECQVTTYYYVGFAYLMILRYQE>XXXXXANILLSMFQRT

Parental  KSMFQRTTYKYEMIN
          K..........E...
Retrocopy KYKYEMINKQNEQMH

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_1585 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1585 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,