RetrogeneDB ID: retro_mdom_392

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:378335414..378336296(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000007025
• Aliases: None
• Description: None

Sequence

>retro_mdom_392
CTGACCTAAGGATATTCTAAGGATGTCTGGTTTAATATGTTAAAAAAGGAGACCAAATATGTTCATGATAAACATTTTGA
AATGCTACATTCTGACTTAGAACCACAGAGGGGATCAATACTTCTAGACTGGCTTTTAGAGGTATGGGAAGTGTACATAC
TACACAGGGAAACATTTTATCTTACTCAAGATTTTTTTGGTAGATTTATGTTGACACAAAAGGATATAAACAAAAATATG
CTTCAGCTTATTGGTATTACTTCATTATTCATTGCTGCAAAACTTGGGGAAATCTATGCTCCTAAATTATAAGAATTTGC
TTATGTTACTGATGGTGCTTTCAGTGAAGATGATATCCTAGGGATTGAACTCATTATATTAAAGGCTTTAAAGTGGGAGC
TCTGTCCAGTAACAATTATTGCCTGGTTGAATGTCTTTCTCCAAATCGATGCTCTAAAAGATGTTCCTAAAGTACTTCTA
CCTCAGTATTCCCAGGAAAAGTTTGCTCAAATAGCCCAGCTCCTAGATCTGTGTATTCTCTCTACTGACTCATTAGAATT
CCAGTATAGAACATTGGCAGCAGCTTTATGTCATTTTATTTCCATTGAAGTTGTTAATAAAGAGTCAGGTTTAAACTGGG
ACAATATTTCAGAATGTGTAGAATGGATGGTTCCTTTTGCCAGAGTAGTGAAGAGTGAACCTCCGGTGAAACTGAAGATT
TTTAAGAAGATTTCTGAAGAAGTCAGATATAATATCCAGACACACACAAATTATCTGGCTATGCTGGAAGTCAATTATGT
GCCAGCTTTCACAAAGGTGGGACAATTGTCACCAATGTGCAACAGAGGCACCACGACAGCACAGAAAAATCCCCAGGAAA
AC

Alignment

ORF - retro_mdom_392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.15 %
• Parental protein coverage: 57.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSWGCSKDVWFNMLKKETKYVHDKHFEMLHSDLEPQMRSILLDWLLEVCEVYTLHRETFYLAQDFFDRFM
          L..G.SKDVWFNMLKKETKYVHDKHFEMLHSDLEPQ..SILLDWLLEV.EVY.LHRETFYL.QDFF.RFM
Retrocopy LT*GYSKDVWFNMLKKETKYVHDKHFEMLHSDLEPQRGSILLDWLLEVWEVYILHRETFYLTQDFFGRFM

Parental  LTQKDINKNMLQLIGITSLFIAAKLEEIYAPKLQEFAYVTDGACSEDDILGMELIILKALKWELCPVTVI
          LTQKDINKNMLQLIGITSLFIAAKL.EIYAPKL.EFAYVTDGA.SEDDILG.ELIILKALKWELCPVT.I
Retrocopy LTQKDINKNMLQLIGITSLFIAAKLGEIYAPKL*EFAYVTDGAFSEDDILGIELIILKALKWELCPVTII

Parental  AWLNVFLQVDALKDVPKVLLPQYSQEKFVQIAQLLDLCILSIDSLEFQYRILAAAALCHFTSIEVVKKAS
          AWLNVFLQ.DALKDVPKVLLPQYSQEKF.QIAQLLDLCILS.DSLEFQYR.L.AAALCHF.SIEVV.K.S
Retrocopy AWLNVFLQIDALKDVPKVLLPQYSQEKFAQIAQLLDLCILSTDSLEFQYRTL-AAALCHFISIEVVNKES

Parental  GLDWDNISECVEWMVPFARVVKGGPPVKLKIFKKISVEDRHNIQTHTNYLAMLEEVNYVSAFTKVGQLSP
          GL.WDNISECVEWMVPFARVVK..PPVKLKIFKKIS.E.R.NIQTHTNYLAML.EVNYV.AFTKVGQLSP
Retrocopy GLNWDNISECVEWMVPFARVVKSEPPVKLKIFKKISEEVRYNIQTHTNYLAML-EVNYVPAFTKVGQLSP

Parental  VCNGGIMTPPKSTEKS
          .CN.G..T..K.....
Retrocopy MCNRGTTTAQKNPQEN

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	0.12 RPM	0.00 RPM
SRP007412_cerebellum	0.65 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_392 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_392 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013401	1 retrocopy	retro_cpor_1278,
Monodelphis domestica	ENSMODG00000007025	2 retrocopies	retro_mdom_392 , retro_mdom_707,
Monodelphis domestica	ENSMODG00000018931	1 retrocopy	retro_mdom_1309,
Otolemur garnettii	ENSOGAG00000034667	1 retrocopy	retro_ogar_1793,