RetrogeneDB ID: retro_mdom_965

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:50023503..50024670(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMU1
• Ensembl ID: ENSMODG00000003439
• Aliases: None
• Description: smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans) [Source:HGNC Symbol;Acc:18247]

Sequence

>retro_mdom_965
ATGTCTACTGAGATTGAGTCTTCCGATGTTATACGTCTCATCATGCAGTACTTGAAGGAAAATAGTTTGCATCGAGCATT
AGCCACTTTGCAGGAGGAGACAACGGTATCCTTGAATACTGTGGACAGCATAGAGAGTTTTGCAGCAGATATTAACAGTG
GACATTGGGATACTGTTTTGCAAGCTATACAGTCCCTGAAATTGCCAGACAAAACACTGGTTGACCTCTATGAACAGGTT
GTTCTAGAATTGATAGAACTTCGTGAATTGGGTGCTGCCAGATCTCTTCTGAGACAGACTGACCCCATGATCATGTTAAA
ACAAACTTGGTCAGAGAGATACATTCATCTTGAGAACCTTTTGGCCAGATCCTATTTTGATCCTCATGAGGCATACCCAG
TTGGAAGCGGCAAGAACAGAAGAGCAGCAATTGCACAGGCTTTAGCTGGAGAAGTCAGTGTTGTACCTCCATCTCGACTT
ACGGCACAGTTGGGACAGGCTTTGAAGTGGCAACAGCACCAAGGTTTGCTTCCTCCTGGTATGACAATTGATTTATTTAG
AGGCAAAGCAGCTGTAAAAGATGTGGAAGAAGAGAAGTTTCCAACATAGTTAAGCAGGCATATTAAATTTGGCCAGAAAT
CACATGTGGAACGTGCTTGATTTTCTCCGGATGGCCAGTATTTGGTCACTGGATCTGTTGATGGTTTCATTGAAGTATGG
AACTTTACAACTGGAAAGATTAGGAAGGATCTCAAGTACCAGGCACAAGATAATTTTATGCTGATGGATGATGCCGTACT
ATGTATGTGTTTCAGCAGAGATACAGAAATGTTAGCAACTGGGGCCCAAGATGGAAAAATTAAGGTATGGAGGATACAGA
GTGGACAATGTTTAAGGAGATTTGAAAGGGCACACAGTAAAGGTGTCACCTGCCTAAGCTTCTCCAAGGATAGCAGTCAG
AATCTCAGTACTTCCTTTGACCAAACAATCAGAATTCATGGCTTAAAATCTGGGAAAACCTTGAAGGAATTTCGTGGTCA
TTCTTCATTTGTTAATGAAGCTACTTTTTCTTAAGATGAATATTATATAATCAGTGCATCATCTGATGGCACTGTGAAGA
TTTGGAATATGAAGACCACCGAGTGTTCAAATACCTTCAATCAAATC

Alignment

ORF - retro_mdom_965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.59 %
• Parental protein coverage: 76.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSIEIESSDVIRLIMQYLKENSLHRALATLQEETTVSLNTVDSIESFVADINSGHWDTVLQAIQSLKLPD
          MS.EIESSDVIRLIMQYLKENSLHRALATLQEETTVSLNTVDSIESF.ADINSGHWDTVLQAIQSLKLPD
Retrocopy MSTEIESSDVIRLIMQYLKENSLHRALATLQEETTVSLNTVDSIESFAADINSGHWDTVLQAIQSLKLPD

Parental  KTLIDLYEQVVLELIELRELGAARSLLRQTDPMIMLKQTQPERYIHLENLLARSYFDPREAYPDGSSKEK
          KTL.DLYEQVVLELIELRELGAARSLLRQTDPMIMLKQT..ERYIHLENLLARSYFDP.EAYP.GS.K..
Retrocopy KTLVDLYEQVVLELIELRELGAARSLLRQTDPMIMLKQTWSERYIHLENLLARSYFDPHEAYPVGSGKN-

Parental  RRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLPPGMTIDLFRGKAAVKDVEEEKFPTQLSRHIK
          RRAAIAQALAGEVSVVPPSRL.A.LGQALKWQQHQGLLPPGMTIDLFRGKAAVKDVEEEKFPT.LSRHIK
Retrocopy RRAAIAQALAGEVSVVPPSRLTAQLGQALKWQQHQGLLPPGMTIDLFRGKAAVKDVEEEKFPT*LSRHIK

Parental  FGQKSHVECARFSPDGQYLVTGSVDGFIEVWNFTTGKIRKDLKYQAQDNFMLMDDAVLCMCFSRDTEMLA
          FGQKSHVE.A.FSPDGQYLVTGSVDGFIEVWNFTTGKIRKDLKYQAQDNFMLMDDAVLCMCFSRDTEMLA
Retrocopy FGQKSHVERA*FSPDGQYLVTGSVDGFIEVWNFTTGKIRKDLKYQAQDNFMLMDDAVLCMCFSRDTEMLA

Parental  TGAQDGKIKVWKIQSGQCLRRFERAHSKGVTCLSFSKDSSQILSASFDQTIRIHGLKSGKTLKEFRGHSS
          TGAQDGKIKVW.IQSGQCLRRFERAHSKGVTCLSFSKDSSQ.LS.SFDQTIRIHGLKSGKTLKEFRGHSS
Retrocopy TGAQDGKIKVWRIQSGQCLRRFERAHSKGVTCLSFSKDSSQNLSTSFDQTIRIHGLKSGKTLKEFRGHSS

Parental  FVNEATFTQDGHYIISASSDGTVKIWNMKTTECSNTFKSL
          FVNEATF..D..YIISASSDGTVKIWNMKTTECSNTF...
Retrocopy FVNEATFS*DEYYIISASSDGTVKIWNMKTTECSNTFNQI

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_965 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_965 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006212	1 retrocopy	retro_cpor_819,
Dipodomys ordii	ENSDORG00000006011	2 retrocopies	retro_dord_126, retro_dord_137,
Echinops telfairi	ENSETEG00000007953	1 retrocopy	retro_etel_1686,
Homo sapiens	ENSG00000122692	1 retrocopy	retro_hsap_457,
Gorilla gorilla	ENSGGOG00000014802	1 retrocopy	retro_ggor_440,
Myotis lucifugus	ENSMLUG00000016097	1 retrocopy	retro_mluc_213,
Monodelphis domestica	ENSMODG00000003439	1 retrocopy	retro_mdom_965 ,
Monodelphis domestica	ENSMODG00000010776	2 retrocopies	retro_mdom_441, retro_mdom_460,
Ochotona princeps	ENSOPRG00000011389	2 retrocopies	retro_opri_19, retro_opri_741,
Pongo abelii	ENSPPYG00000019140	1 retrocopy	retro_pabe_274,
Pan troglodytes	ENSPTRG00000020853	1 retrocopy	retro_ptro_344,