RetrogeneDB ID: retro_mdom_152

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:284710656..284711868(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000011739
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013057
• Aliases: None
• Description: None

Sequence

>retro_mdom_152
ATGGCTGACTTGCAGAAGACCCAGAAGCAGAAAGACAAAATGGAAATACAGCAGAGTGGGGAAGACAATGGCTATCTACT
AAAAGATAAAGATGATTCTTTGGACAATGATATTAAAGTTTTCAAAAGTCCAAATAAGGAAAATAAAAAGAAAGACAAAG
ATATGCTTGAAGATAAATTTAAAAACAATAACTTAGAAAGGGAACAAGAGCAAATTGACCGTATTGTTAAAGAATCTGGG
GGAAAGTTGACCAGAAGGCTTATAAATAGTCAGTGTGAGTTTGAAAGAAGAAAGCCAGATGGAACCACAACATTAGGACT
TCTTAATCCTGTGGACCCTATTGCAGGAGAACCTGGCTATTGTCCTGTAAGATTGGGAATGACAACTGGAAGACTTCAGT
CTGGAGTTAATACACTGCAGGGGTTCAAAGAGGACAAAAGGAATAAAGTTACTCCAGTGTTATACTTGAATTATGGACCC
TACAGTTCTTATGCACCAAACTATGATTCTACATTTGCAAATATCAGCAAGGATGATTCTGATTTAATCTACACAATTTA
TGGGGAAGATTCTAATCTTTCAGGTGGTTTCAGTATCCATGAGTTTTTGGCCACATCACAAGATTATCCATATGTTATGG
CAGACAGTTTATTGGATGTTCTAACAAAAGGAGGACATTCTCGATCCCTCAGAGAGCTTGAGATGGCAGCACCTGAAGGT
GAAACCCAGAATGGTAGTCTTGACAGTGCAAAAGACATGGAGGTTACAGAAACAGACTCAGCTGGTTCTTTGGACTCTAG
TACTAATAAGGACAGACTTACAGCACTAAATGCAGTAACAAACTTTGGAGCCCAGATTGAGATTTTTGATTCTGAAGAGG
CTGAAGTATTCCAGAGAAAACTTGATGAAACCACTAAATTACTAAGAGAACTTCAAGAGGCTCAGAATGAACGTCTGAGT
ACCAGACCTCCTCCTAATATGATTTGCCTTTTGGGACCATCTTACAGAGAAATGCATTTGGCTGAACAGGTGGCCAACAA
TCTAAAAGAACTTGCACAGCAAGTAACTCCAGGTGACATAGTAAGCATGTATGGAATCCGGAAAGCAATGGGGATTTCCA
TTCCTTCTCCTGTCATAGACAACAGCTTCATAGATTTAACAGAAGATCTTGAAGAACCAAAAAAAATCAGCACCACTGAA
TGTGGGGGATCT

Alignment

ORF - retro_mdom_152 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.52 %
• Parental protein coverage: 61.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADLQKTRKQKDKMEIQQSGEDNGYLLKDKDDSLDNDIKVFKSPNKENKKKDKDMLEDKFKNNNLEREQE
          MADLQKT.KQKDKMEIQQSGEDNGYLLKDKDDSLDNDIKVFKSPNKENKKKDKDMLEDKFKNNNLEREQE
Retrocopy MADLQKTQKQKDKMEIQQSGEDNGYLLKDKDDSLDNDIKVFKSPNKENKKKDKDMLEDKFKNNNLEREQE

Parental  QIDRIVKESGGKLTRRLINSQCEFERRKPDGTTTLGLLNPVDPIAGEPGYCPVRLGMTTGRLQSGVNTLQ
          QIDRIVKESGGKLTRRLINSQCEFERRKPDGTTTLGLLNPVDPIAGEPGYCPVRLGMTTGRLQSGVNTLQ
Retrocopy QIDRIVKESGGKLTRRLINSQCEFERRKPDGTTTLGLLNPVDPIAGEPGYCPVRLGMTTGRLQSGVNTLQ

Parental  GFKEDKRNKVTPVLYLNYGPYSSYAPNYDSTFANISKDDSDLIYTTYGEDSNLSGGFSIHEFLATSQDYP
          GFKEDKRNKVTPVLYLNYGPYSSYAPNYDSTFANISKDDSDLIYT.YGEDSNLSGGFSIHEFLATSQDYP
Retrocopy GFKEDKRNKVTPVLYLNYGPYSSYAPNYDSTFANISKDDSDLIYTIYGEDSNLSGGFSIHEFLATSQDYP

Parental  YVMADSLLDVLTKGGHSRSLRELETAAPEGETQNGSLDSAKDMEVTETDSAGSLDSSTNKDRLTALKAVT
          YVMADSLLDVLTKGGHSRSLRELE.AAPEGETQNGSLDSAKDMEVTETDSAGSLDSSTNKDRLTAL.AVT
Retrocopy YVMADSLLDVLTKGGHSRSLRELEMAAPEGETQNGSLDSAKDMEVTETDSAGSLDSSTNKDRLTALNAVT

Parental  NFGAQIEIFDSEAEAEVFQRKLDETTKLLRELQEAQNERLSTRPPPNMICLLGPSYREMHLAEQVTNNLK
          NFGAQIEIFDSE.EAEVFQRKLDETTKLLRELQEAQNERLSTRPPPNMICLLGPSYREMHLAEQV.NNLK
Retrocopy NFGAQIEIFDSE-EAEVFQRKLDETTKLLRELQEAQNERLSTRPPPNMICLLGPSYREMHLAEQVANNLK

Parental  ELAQQVTPGDIVSMYGIRKAMGISIPSPVIDNSFIDLTEDLEEPKKISTTECGGS
          ELAQQVTPGDIVSMYGIRKAMGISIPSPVIDNSFIDLTEDLEEPKKISTTECGGS
Retrocopy ELAQQVTPGDIVSMYGIRKAMGISIPSPVIDNSFIDLTEDLEEPKKISTTECGGS

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	4.05 RPM	97.15 RPM
SRP007412_cerebellum	2.29 RPM	62.03 RPM
SRP007412_heart	0.40 RPM	38.67 RPM
SRP007412_kidney	2.63 RPM	90.86 RPM
SRP007412_liver	3.02 RPM	67.97 RPM
SRP007412_testis	4.13 RPM	145.75 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_152 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_152 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009355	1 retrocopy	retro_chof_2431,
Callithrix jacchus	ENSCJAG00000001832	1 retrocopy	retro_cjac_2372,
Homo sapiens	ENSG00000166164	2 retrocopies	retro_hsap_2723, retro_hsap_3507,
Gorilla gorilla	ENSGGOG00000014824	2 retrocopies	retro_ggor_1895, retro_ggor_2372,
Monodelphis domestica	ENSMODG00000013057	1 retrocopy	retro_mdom_152 ,
Otolemur garnettii	ENSOGAG00000011289	2 retrocopies	retro_ogar_326, retro_ogar_438,
Pan troglodytes	ENSPTRG00000008103	3 retrocopies	retro_ptro_1840, retro_ptro_2379, retro_ptro_2384,