RetrogeneDB ID: retro_mdom_30

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:125239695..125240349(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000008129
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019402
• Aliases: None
• Description: None

Sequence

>retro_mdom_30
ATGGCTGCCTCCAGCCAGTTGTGGTTGTTACTGGCTTTTCTCTGTGCCTCCGACCTGCTCCAGTACTTAATCTCGGCTAA
AGAGGCCACGAAGGAGGAGACCCAGCCACCTCTGCTTCAGAAGAAGAAAAAAAACATTCTTCAGTACAACGATGAGGACA
TGGAGCAGCTGCTGAAGCAATGGGAAAAAGATGATGTTTTAGAAGAATGGGAGCTTCCCCAACAACGAAAACCACTAGAT
ACCTCTCAAGCTGCACCTGGCAAGCCGGACAGCGTTCTGAAAATGACGAAAAAGGGAAAAACCCTTATAATGTTTGCAAC
AGTGTCAGGAAATCCCACAAAAAAGGAGACGCAAGAAATAGGAGGCTTATGGCAGTGGAGCCTTTTCAATGCCAACTATA
ACCTCCAAAGAGTTACTGTTGGGACAGATGTTGTCATCTTCATGCTTCCTGATGGGAGCAAAGCCTGGGAGATCAAAGAA
TTTTTGGTAAATCAAGACAGATGTGCCGATGTGACTCTACAAGGGCGGGTATACCCTGGCAAAGGAGGAAGTAAAAACCA
AACGAAAGCATCGGTCAAGAAAAAGGAGGCAGATGAGAAAACTAGGTCCTTTAAAGAAGTTAGTCGAGGAATAAGGCGGA
GAGATGACCTATGA

Alignment

ORF - retro_mdom_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAFRWQCLALALFFTSDLLFCLVSADEDTKATAQPHP-PRKKKDIRDYNDADMARLLEQWEKDDDIEEG
          MAA.....L.LA....SDLL..L.SA.E.TK...QP.....KKK.I..YND.DM..LL.QWEKDD..EE.
Retrocopy MAASSQLWLLLAFLCASDLLQYLISAKEATKEETQPPLLQKKKKNILQYNDEDMEQLLKQWEKDDVLEEW

Parental  DLPEHKRPSPPIDFSQIDPGKPESILKMTKKGKTLMMFATVSGNPTEKETEEITSLWQGSLFNANYDVQR
          .LP.......P.D.SQ..PGKP.S.LKMTKKGKTL.MFATVSGNPT.KET.EI..LWQ.SLFNANY..QR
Retrocopy ELPQQRK---PLDTSQAAPGKPDSVLKMTKKGKTLIMFATVSGNPTKKETQEIGGLWQWSLFNANYNLQR

Parental  FIVGSDRAIFMLRDGSYAWEIKDFLISQERCADVTVEGQVYPGKGGSKFKNKTKPENKKKGDKTRSFKED
          ..VG.D..IFML.DGS.AWEIK.FL..Q.RCADVT..G.VYPGKGGSK...K.....K....KTRSFKE.
Retrocopy VTVGTDVVIFMLPDGSKAWEIKEFLVNQDRCADVTLQGRVYPGKGGSKNQTKASVKKKEADEKTRSFKEV

Parental  NRSSRQRDDL
          .R..R.RDDL
Retrocopy SRGIRRRDDL

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	104.77 RPM
SRP007412_cerebellum	0.00 RPM	79.00 RPM
SRP007412_heart	0.00 RPM	81.14 RPM
SRP007412_kidney	0.00 RPM	243.61 RPM
SRP007412_liver	0.00 RPM	135.94 RPM
SRP007412_testis	0.00 RPM	116.09 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_30 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_30 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007811	1 retrocopy	retro_cjac_3285,
Homo sapiens	ENSG00000117899	1 retrocopy	retro_hsap_990,
Gorilla gorilla	ENSGGOG00000027583	1 retrocopy	retro_ggor_793,
Loxodonta africana	ENSLAFG00000014513	1 retrocopy	retro_lafr_505,
Monodelphis domestica	ENSMODG00000019402	2 retrocopies	retro_mdom_30 , retro_mdom_344,
Oryctolagus cuniculus	ENSOCUG00000016290	1 retrocopy	retro_ocun_1947,
Pan troglodytes	ENSPTRG00000007366	1 retrocopy	retro_ptro_759,