RetrogeneDB ID: retro_mdom_1247

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:95794584..95795593(+)
• 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_1247
GCCATGTCCTACCTGTCCGAGGGTTACGACAATGAGGCTGCATATGATCCCTATGCTTACCCTGGTGACTATGACATGCA
CACAGGAGACCCAAAGCAGGACCCAGCCTATGAATGACAATATGAGCAGCAGACCTATCAAGTAATTCCAGAAGTGATCA
AGGATTTCATCCAATATTTCCATAAAACCATCTCCAACCTTATTGACCAGAAAGTGTATGAGCTCCAGGAAAGCCAGATG
TCCAACGACATCATTGACCAAAAGTTGCATGAGATCCAGGACATCTATGAGAACAGCTGGCCCAAGCTGACTGAAAGGTT
CTTCAAGAATACCCCCTGGCCAGAAGCAGAGGCCATTGCCCCACAATTTGGCAACGATGCTGTCTTCTTGATCCTGTATA
AGGAATTTTTATTACAGACACATCTATGCCAAAGTCAGTGGCGGGCCTTCCTTGGAACAGAGGTTTGAGTCCTATTACAA
CTACTGCAACCTTTTCAACTTCATTCTCAATGCTGATGGACCTGCTCCCCTTGAACTGCCCAACCAGTGGCTGTGGGATA
TCATTGATGAATTCATCTACCAGTTTCAGTCATTCAGTCAATACTGGTGGAAGACAGCCAAAAAGTCAGATGAAGAGGTT
GACTTTCTTTGTTCCAACCCCAAGGACTGGAATGTCCACAGCATCCTCAATGTGCTTCATTCCCTTGTAGACAAATCCAA
TATCAGCCGGCAGGTAGAAGTCTAAACCAGTGGAGGTGACCCTGAGAGTGTGGCTGGTGAGTATGGCCAGTACTCCCTCT
ACAAGATGCTTGGCTACTTCAGCCTGGTGAGGCGGCTCTGGCTCTACTTCCTCTTGGGGGATTACTACCAGGCTATCAAG
GTGCTAGAGAACATTGAATTGAACAAGAAGAGCATGTATTCCCGGGTGCCTGAATGCCAGGTCACCACCTATTACTATGT
GGGGTTTGCCTACTTGATGATGCGCTGGTACCAGGATGCCATTCATGTC

Alignment

ORF - retro_mdom_1247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.61 %
• Parental protein coverage: 59.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AMSYPSEDYDNEAAYDPYAYPGDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKDFIQYFHKTVSDLIDQ
          AMSY.SE.YDNEAAYDPYAYPGDYDMHTGDPKQD.AYE.QYEQQTYQVIPEVIKDFIQYFHKT.S.LIDQ
Retrocopy AMSYLSEGYDNEAAYDPYAYPGDYDMHTGDPKQDPAYE*QYEQQTYQVIPEVIKDFIQYFHKTISNLIDQ

Parental  KVYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKEL-YYR
          KVYELQ.S..S.D.IDQK..EIQDIYENSW.KLTERFFKNTPWPEAEAIAPQ.GNDAVFLILYKE..YYR
Retrocopy KVYELQESQMSNDIIDQKLHEIQDIYENSWPKLTERFFKNTPWPEAEAIAPQFGNDAVFLILYKEF>YYR

Parental  HIYAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRWKTAKKS
          HIYAKVSGGPSLEQRFESYYNYCNLFN.ILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQY.WKTAKKS
Retrocopy HIYAKVSGGPSLEQRFESYYNYCNLFNFILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYWWKTAKKS

Parental  DEEIDFLRSNPKVWNVHSVLNVLHSLVDKSNINRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLL
          DEE.DFL.SNPK.WNVHS.LNVLHSLVDKSNI.RQ.EV.TSGGDPESVAGEYG..SLYKMLGYFSLV..L
Retrocopy DEEVDFLCSNPKDWNVHSILNVLHSLVDKSNISRQVEV*TSGGDPESVAGEYGQYSLYKMLGYFSLVRRL

Parental  RLHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRV
          .L..LLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMR.YQDAI.V
Retrocopy WLYFLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMRWYQDAIHV

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_1247 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1247 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,