RetrogeneDB ID: retro_mdom_620

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:551945761..551946630(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMADHC
• Ensembl ID: ENSMODG00000003566
• Aliases: None
• Description: methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria [Source:HGNC Symbol;Acc:25221]

Sequence

>retro_mdom_620
ATGGCCAATGTGCTCTGTAGCAGAGCCAGGCTGATTACCTACCTCCCAAGCTTTTACTCTTTAGTCAGGAGGGTTGTAAA
TCCCAAAGCTTTTTCTACTGCTGGATCTTCAAGTTCAGATGAGTCTCATGTAGCTACTACACCCCCAGACATGTTCAAGG
TCTGTGTGGCCAGATGAAACAATGGGATCATTTGGACCCCAGGATCAAAGATTTCAGCTCCCTGGAAATATAGGTTTTGA
TTGTCACCTCAATGGGACAGTTTTGCAGAAGAAAATCCAGTTCATAGAACTTTACCTGATGTCTTAGCAGAGCCTTTATC
AAGTGAAAGGCATGGATTTGTGATGGCACAATATGTAAATGAATTTGAGGGAAGTGATGTACCTGTTGAACAACAGGAAG
TTAACAAAGCAGAAACATTTTGAAAATGCCAAAGTAGAATGTGAACTCCAGACATGCCCAGAACTACTTCGAAAAGATTT
TGAATCAATATTTCCAGAAGTCAAACTAATGGTACTAACTGTAACAGAAAACCAAAAATGATATGACCACATGGAGGTTG
AAAATGAAAGAGAAATGCTGTTAGAAAAGTTCGTAACTGATGCTAAAGAAATTTGCTATGCTTTGCATACTGAAGGCTAT
TGGGCTGACTTTATTGATCCATCATCTGGATTGGCATTTTTTTGGACCATATACAAGCAATACTCTTTTTGAAACAGATG
AGCGATATCGACATTTAGGATTCTCTGTTGATGATCTTGGCTGCTGCAAAGTGATTCGCCATAGTATTTGGGGTACATAT
GTGGTTGTTGGAAGTATCTTCACTAATGCCACACCTGACAGTAGAATTATGAAGAAATTAAGTGGAAAC

Alignment

ORF - retro_mdom_620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MANVLCSRARLVTYLPGFYSLVRRVVNPKAFSTAGSSGSDESHVATTPP-DICSRTVWPDETMGPFGPQD
          MANVLCSRARL.TYLP.FYSLVRRVVNPKAFSTAG.S.S.......T.P...CSR.VWPDETMG.FGPQD
Retrocopy MANVLCSRARLITYLPSFYSLVRRVVNPKAFSTAG-SSSSDESHVATTP>QTCSRSVWPDETMGSFGPQD

Parental  QRFQLPGNIGFDCHLNGTALQKK-NPVHRTLPDVLAEPLSSERHEFVMAQYVNEFEGSDVPVEQ-QEVNK
          QRFQLPGNIGFDCHLNGT.LQKK.NPVHRTLPDVLAEPLSSERH.FVMAQYVNEFEGSDVPVEQ.....K
Retrocopy QRFQLPGNIGFDCHLNGTVLQKK<NPVHRTLPDVLAEPLSSERHGFVMAQYVNEFEGSDVPVEQ>RKLTK

Parental  AETYFENAKVECVLQTCPELLRKDFESIFPEVNSGKLMVLTVTQKTKNDMTTWSEEVENEREMLLEKFIT
          ....FENAKVEC.LQTCPELLRKDFESIFPEV...KLMVLTV...T.N.......EVENEREMLLEKF.T
Retrocopy -QKHFENAKVECELQTCPELLRKDFESIFPEV---KLMVLTV---TENQK*YDHMEVENEREMLLEKFVT

Parental  GAKEICYALRTEGYWADFIDPSSGLA-FFGPYTSNTLFETDERYRHLGFSVDDLGCCKVIRHSIWGTHVV
          .AKEICYAL.TEGYWADFIDPSSGLA.FFGPYTSNTLFETDERYRHLGFSVDDLGCCKVIRHSIWGT.VV
Retrocopy DAKEICYALHTEGYWADFIDPSSGLA>FFGPYTSNTLFETDERYRHLGFSVDDLGCCKVIRHSIWGTYVV

Parental  VGSIFTNATPDSRIMKKLSGN
          VGSIFTNATPDSRIMKKLSGN
Retrocopy VGSIFTNATPDSRIMKKLSGN

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	1.20 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	1.96 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_620 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_620 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003086	2 retrocopies	retro_cjac_4082, retro_cjac_4101,
Cavia porcellus	ENSCPOG00000007690	1 retrocopy	retro_cpor_30,
Homo sapiens	ENSG00000168288	2 retrocopies	retro_hsap_4716, retro_hsap_865,
Gorilla gorilla	ENSGGOG00000027348	1 retrocopy	retro_ggor_704,
Macaca mulatta	ENSMMUG00000005633	1 retrocopy	retro_mmul_1058,
Monodelphis domestica	ENSMODG00000003566	2 retrocopies	retro_mdom_1749, retro_mdom_620 ,
Mustela putorius furo	ENSMPUG00000000323	1 retrocopy	retro_mputfur_1253,
Nomascus leucogenys	ENSNLEG00000010795	2 retrocopies	retro_nleu_1988, retro_nleu_426,
Otolemur garnettii	ENSOGAG00000034385	4 retrocopies	retro_ogar_3266, retro_ogar_356, retro_ogar_688, retro_ogar_813,
Pan troglodytes	ENSPTRG00000012525	1 retrocopy	retro_ptro_599,
Ictidomys tridecemlineatus	ENSSTOG00000021576	1 retrocopy	retro_itri_1809,
Tarsius syrichta	ENSTSYG00000009075	1 retrocopy	retro_tsyr_1690,