RetrogeneDB ID: retro_mdom_707

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:167800370..167801611(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000010401
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_mdom_707
GAACTTTTGAAGAATCCAAAGAAAAAAATGTCAAGACGAAGTAGCCGTTTGCAAGCTAAACAGCAGCCCGAAACTAGTCA
AACAGATTCTCCTCAGGAAACTCAATTCCTTCAAGCCAAAAAAGGAAAACGACTCAGGATGTAAAGAAAAGAAAAGAGGA
GACTGGAGCCAAGAGACAGCAATATGAAATTAGGAATTGTTGGCCACCTGTGTTATCTGGGGGCATCACTCCTTGCATTA
TTATTGAAACCCCACACAAAGAAACTGTCACCAGTGACTTCTCCAGGTTTACTAACTACAGGTTTAAAAACCTTTTCATA
AATCTTTCACCTCTGCCTGACCTAAGTTGGGGATGTGCTAAGGATGTCTGGTTTAATATGTTAAAAAAGGAGACCAAATA
TGTTCATGATAAACATTTTGAAATGCTACATTCTGACTTAGAACCACAGATGAGATCAATACTTCTAGACTGGCTTTTAG
AGGTATGTGAAGTGTACACACTTCACAGGGAAACATTTTATCTTGCTCAAGATTTTTTTGATAGATTTATGTTGACACAA
AAGGATATAAACAAAAATATGCTTCAGATTATTGGTATTACCTCATTATTCATTGCTGCAAAACTTGAGGAAATCTATGC
TCCTAAATTACAAGAATTTGCTTATGTTACTGATGGTGCTTGCAGTGAAGATGATATCCTAGGGATGGAACTCATTATAT
TAAAGGCTTTAAAGTGGGAGCTGTGTCCAGTAACAGTTATTGCCTGGTTGAATGTCTTTCTCCAAGTCGATGCTCTAAAA
GATGTTCCTAAAGTACTCCTACCTCAGTATTCCCAGGAAAAGTTTGTTCAAATAGCCCAGCTCCTGGATCTGTGTATTCT
CTCTATTGACTCATTAGAATTCCAGTATAGAATATTGGCAGCAGCTGCTTTATGCCATTTTACCTCCATTGAAGTTGTTA
AGAAAGCTTCAGGTTTAGACTGGGACAACATTTCAGAATGTATAGAATGGATGGTACCTTTTGCCAGAGTAGTGAAGGGT
GGACCTCTGGTGAAACTGAAGATTTTTAAGAAGATTTCTGTAGAAGATAGACATAATATCCAGACACACACAAATTATTT
GGCTATTCTGGAGGAAGTCAATTATGTGTCAGCTTTCACAAAGGTGGGACAATTGTCAGCAGTGTGCAACTGAGGCATCA
TGACACCACCAAAGAGCACAGAAAAATCCCCAGGAAAACAC

Alignment

ORF - retro_mdom_707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.59 %
• Parental protein coverage: 80.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELLKNPKKKMSRRSSRLQAKQQPQTSQTDSPQETQFLQAKK-RKTTQDVKKRKEETGAKRQQYEIRNCWP
          ELLKNPKKKMSRRSSRLQAKQQP.TSQTDSPQETQFLQAKK.RKTTQDVKKRKEETGAKRQQYEIRNCWP
Retrocopy ELLKNPKKKMSRRSSRLQAKQQPETSQTDSPQETQFLQAKK<RKTTQDVKKRKEETGAKRQQYEIRNCWP

Parental  PVLSGGITPCIIIETPHKETVTSDFSRFTNYRFKNLFINPSPLPDLSWGCSKDVWFNMLKKETKYVHDKH
          PVLSGGITPCIIIETPHKETVTSDFSRFTNYRFKNLFIN.SPLPDLSWGC.KDVWFNMLKKETKYVHDKH
Retrocopy PVLSGGITPCIIIETPHKETVTSDFSRFTNYRFKNLFINLSPLPDLSWGCAKDVWFNMLKKETKYVHDKH

Parental  FEMLHSDLEPQMRSILLDWLLEVCEVYTLHRETFYLAQDFFDRFMLTQKDINKNMLQLIGITSLFIAAKL
          FEMLHSDLEPQMRSILLDWLLEVCEVYTLHRETFYLAQDFFDRFMLTQKDINKNMLQ.IGITSLFIAAKL
Retrocopy FEMLHSDLEPQMRSILLDWLLEVCEVYTLHRETFYLAQDFFDRFMLTQKDINKNMLQIIGITSLFIAAKL

Parental  EEIYAPKLQEFAYVTDGACSEDDILGMELIILKALKWELCPVTVIAWLNVFLQVDALKDVPKVLLPQYSQ
          EEIYAPKLQEFAYVTDGACSEDDILGMELIILKALKWELCPVTVIAWLNVFLQVDALKDVPKVLLPQYSQ
Retrocopy EEIYAPKLQEFAYVTDGACSEDDILGMELIILKALKWELCPVTVIAWLNVFLQVDALKDVPKVLLPQYSQ

Parental  EKFVQIAQLLDLCILSIDSLEFQYRILAAAALCHFTSIEVVKKASGLDWDNISECVEWMVPFARVVKGGP
          EKFVQIAQLLDLCILSIDSLEFQYRILAAAALCHFTSIEVVKKASGLDWDNISEC.EWMVPFARVVKGGP
Retrocopy EKFVQIAQLLDLCILSIDSLEFQYRILAAAALCHFTSIEVVKKASGLDWDNISECIEWMVPFARVVKGGP

Parental  PVKLKIFKKISVEDRHNIQTHTNYLAMLEEVNYVSAFTKVGQLSPVCNGGIMTPPKSTEKSPGKH
          .VKLKIFKKISVEDRHNIQTHTNYLA.LEEVNYVSAFTKVGQLS.VCN.GIMTPPKSTEKSPGKH
Retrocopy LVKLKIFKKISVEDRHNIQTHTNYLAILEEVNYVSAFTKVGQLSAVCN*GIMTPPKSTEKSPGKH

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_707 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_707 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,