RetrogeneDB ID: retro_mdom_1309

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:399794823..399795942(+)
• Located in intron of: ENSMODG00000023652

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018931
• Aliases: None
• Description: None

Sequence

>retro_mdom_1309
GCACCCCCGAAGCCCAAGCGCCAGTCCATTGTTGGTCCTCTCAGAGACATTCCTGTTAATGACGAGCAGGGTACTGGCCC
AGCTTGGAATGCCACCAGTAAGAAGGCTGCTTTCATCATTCAAGTGCATGAACCAGAGTATAAGAATGGAAAGACATTTC
TTATTGGCCCAAAAGTGCTGTGTGAGGATGATGTGCTGGGTTTCAATTCAGCTGTTTCCCTGCCAGAGACAAGAAAGCCT
TTGGTGCCCCTTGATTATCCAATGGGGGATTGTCTTGAATCCGCCATTACTATGGACACATCCATGGTCCTGGAAGCAGA
TGGAAAGCCGCCCAATAGCAATGAAATCCTTGACTACCAGGAAGACATCCATCTGTACCTCAGGAAAATGGAGGTGAAAT
ACAAACCTAAAGTAGGTTACATGATGAAGCAACCAGTCATAACCAACCATATGAGGGCTGTCTTGGTGGACTGGCTAGTG
GAAGCTGGGGAGGAATACAGTTTCCAGAATGAGACTCTCCATTTGGCTGTGAACTATATTGATAGATATCTTTCTTCGGT
GTTAGTTTCGCGGGGAAAACTTCAGCTAGTTGGGACTGCCGCCATGTTCATTGCCTCAAAGTTTGAGGAAATGTGTCCAC
CAAATGTGGCCGAATTTGTGTACCTCGCAAATGACCAGTACACAAAAAGTCAGGTCATAGGAATGGAGCAAATGATGCTG
AACGTGCTGGCTTTTGACCTCGGAGCACCAACAGTAATCCAGTTCCTCGCTCATTATTTCATGCATCAGCAGCAGGCCAA
TTCTAAGGTGGAAAGTTTAGCAATGTTTCTGGGAGAGTTGAGTTTAATTGATGCTGACCCATACCTGAAATATTTACCCT
CAGTGACCGCTGGAGCTGCCTTTCATCTCGCACTCTACACAATCACTGGGAAAAGCTGGCCCGAGTCATTGAGCCAAAAA
ACGGGCTACACCTTGGAAAGTCTTAAGCCATGTCTAATGGACCTTCATCAGACCTACCTCAGAGCACCACATCGTGCCCT
ACAGGGCATGCAAGAAAAATACAAGAAGGCAAAGTACCACTGCGTATCCCTCATCAGTCCTCCAGAGACACTAAACTTA

Alignment

ORF - retro_mdom_1309 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.92 %
• Parental protein coverage: 88.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APHKSKNRRVAAPLRDVPLHDEPGIVPAWNAPSKQPAFTIHVDEPEGETGKK-LPGPKKGESEDLLGFNS
          AP.K.K......PLRD.P..DE.G..PAWNA.SK..AF.I.V.EPE...GK..L.GPK.....D.LGFNS
Retrocopy APPKPKRQSIVGPLRDIPVNDEQGTGPAWNATSKKAAFIIQVHEPEYKNGKTFLIGPKVLCEDDVLGFNS

Parental  AVSLPE-RKPLGPLDYPMDGSFESPLTMDMSVVLEPEERPPNVNEVPDYHEDIYLYLREMEVKCKPKAGY
          AVSLPE.RKPL.PLDYPM....ES..TMD.S.VLE....PPN.NE..DY.EDI.LYLR.MEVK.KPK.GY
Retrocopy AVSLPETRKPLVPLDYPMGDCLESAITMDTSMVLEADGKPPNSNEILDYQEDIHLYLRKMEVKYKPKVGY

Parental  MKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSAMSVLRGKLQLVGTAAMLLASKFEE
          M.KQP.ITN.MRA.LVDWLVE.GEEY..QNETLHLAVNYIDR.LS...V.RGKLQLVGTAAM..ASKFEE
Retrocopy MMKQPVITNHMRAVLVDWLVEAGEEYSFQNETLHLAVNYIDRYLSSVLVSRGKLQLVGTAAMFIASKFEE

Parental  IYPPEVAEFVYITDDTYNKKQVLRMEHLVLKVLAFDLAAPTINQFLTQYFLHQQQANSKVESLAMFLGEL
          ..PP.VAEFVY...D.Y.K.QV..ME...L.VLAFDL.APT..QFL..YF.HQQQANSKVESLAMFLGEL
Retrocopy MCPPNVAEFVYLANDQYTKSQVIGMEQMMLNVLAFDLGAPTVIQFLAHYFMHQQQANSKVESLAMFLGEL

Parental  SLIDADPYLKYLPSVTAGAAFHIALYTITGKSWPESLIQKTGYTLETLKPCLMDLHQTYLRAPHHLQQSI
          SLIDADPYLKYLPSVTAGAAFH.ALYTITGKSWPESL.QKTGYTLE.LKPCLMDLHQTYLRAPH...Q..
Retrocopy SLIDADPYLKYLPSVTAGAAFHLALYTITGKSWPESLSQKTGYTLESLKPCLMDLHQTYLRAPHRALQGM

Parental  REKYKTAKYHGVSLINPPETLNL
          .EKYK.AKYH.VSLI.PPETLNL
Retrocopy QEKYKKAKYHCVSLISPPETLNL

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_1309 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1309 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004943	1 retrocopy	retro_btau_1335,
Macropus eugenii	ENSMEUG00000000128	1 retrocopy	retro_meug_32,
Myotis lucifugus	ENSMLUG00000005161	1 retrocopy	retro_mluc_400,
Monodelphis domestica	ENSMODG00000007025	2 retrocopies	retro_mdom_392, retro_mdom_707,
Monodelphis domestica	ENSMODG00000018931	1 retrocopy	retro_mdom_1309 ,
Oryctolagus cuniculus	ENSOCUG00000028042	1 retrocopy	retro_ocun_169,