RetrogeneDB ID: retro_mdom_21

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:136506068..136507652(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000005248
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018500
• Aliases: None
• Description: None

Sequence

>retro_mdom_21
ATGGTGGCTCATGATGAGATTGGAAGTTTTCTGCCTATTAAAAGGACTATTCGTGTCCTCGATGTTAATAATCAGTCCTT
TAGAGAACAAGAGGAGCCAAGCAACAAAAGAGTTCGATCTCTGGCTCGAGTCTCATCTTTGGCAAATTTAATCTCTCCTG
TGAGAAATGGAGCAGTCAAACGTTTTGGTCAAACGATACAGAAATCATTTAACAGGGCTACTGTCCCAACTCCTTCTAAA
AGAAGAAACAGTGTACGATGGTCAGAGATGTTAGATATCAACATGAAAGAATCTTTAACCACCAAAGAAATCAAACGTCA
AGAGGCAATATATGAAATGCTCCAAGGAGAACAGGATTTAATTGAGGATCTTAAGCTTGCCAGAAAGGCCTACCATGATC
CTATGTTGAAGTTATCTATCATGTCTGAGGAAGAACTCACACATATATTTGGAGATTTAGATGCTTACATACCTCTGCAT
GAAGATCTGTTGGCAAGATTAGGAGAAGCAACAAAGCCAGATGGGACAGTGGAGCAAATTGGTCATATTCTTGTGAACTG
GTTGCCAGGTTTAAATGCTTATAGAGGCTACTGCAGTAACCAGCTTGCAGCTAAAGCTCTTCTTGATCAGAAAAAACAAG
ATGCAAGAGTTCAAGATTTCCTTCAGCGTTGTCTTGAGTCTCCTTTCAGTAGGAAATTAGACCTCTGGAGTTTCCTGGAC
ATTCCTCGAAGTCACCTAGTTAAATATCCCTTGTTGTTAAAAGAAATTCTCAGACATACACCCAAAGACCACACTGATAT
AAAACCTCTAGAAGAAGCTCTATTGGTAATACAAGGAGTACTCTCTGATATCAACTTGAAGAAAGGAGAATCAGAATGCC
AATATTATATTGATAAACTGGAATATCTGGATGACAAACAGAAGGATCCTAGGATTGAAGCTAGCAAGGTGTTGCTTTGC
CATGGAGAACTGAAGAATAAAAATGGACATAAACTCTATATTTTCTTGTTTCAAGACATCCTTGTCTTGACTCGTCCTGT
TATACGCAATGAACGCCACTCCTATCAAGTATACCGTCAGCCTATTCCTGTCAAGGAGCTGGTGTTAGAGGACCTGCAGG
ATGGTGATGTGAGAATGGGAGGTTCCTTTAGAGGTGCTTTTAGCAACTCAGACAAAGCTAAAAATATCTTCAGAGTTCGT
TTCCGGGACCCTTCACCAGGGCAGTCCCATACTTTACAAGCTAATGATGTGTTCCATAAGCAACAGTGGTTCAATTGTAT
CCGAACTGCCATTGCCCCCTTTCATCAGACCACCAGTCCAACAGAGTTTAAGGGTTTGTCGGAGCTCAATAAGGGGTCTG
AAAAGAACAACCCTTTGGCATCACACATCAAATCCCAAAGGAAGTCATCAACACTTTCTGGTCTCATTCCTCTGGAAGTA
GATGAAAATTCCCCTGAATGTATTCCCAGCATAGCTATAAATGAAAACTCCACAGATATAAAAGCACACAGAATACAACC
TGGGTCCCCAAAAGCACAAGAGAAGGCCCAACTGAATGATAAAAGGAAAGAGACTTTGGTATAA

Alignment

ORF - retro_mdom_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.57 %
• Parental protein coverage: 72.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKSFNRATVPTPSKRRNSVRWSEMLDINMKESLTTKEIKRQEAIYEMLRGEQDLIEDLKLARKAYHDPML
          QKSFNRATVPTPSKRRNSVRWSEMLDINMKESLTTKEIKRQEAIYEML.GEQDLIEDLKLARKAYHDPML
Retrocopy QKSFNRATVPTPSKRRNSVRWSEMLDINMKESLTTKEIKRQEAIYEMLQGEQDLIEDLKLARKAYHDPML

Parental  KLSIMSEEELTHIFGDLDAYIPLHEDLLARLGEATKPDGTVEQIGHILVNWLPGLNAYRGYCSNQLAAKA
          KLSIMSEEELTHIFGDLDAYIPLHEDLLARLGEATKPDGTVEQIGHILVNWLPGLNAYRGYCSNQLAAKA
Retrocopy KLSIMSEEELTHIFGDLDAYIPLHEDLLARLGEATKPDGTVEQIGHILVNWLPGLNAYRGYCSNQLAAKA

Parental  LLDQKKQDARVQDFLQRCLESPFSRKLDLWSFLDIPRSRLVKYPLLLKEILRHTPKDHTDIKPLEEALLV
          LLDQKKQDARVQDFLQRCLESPFSRKLDLWSFLDIPRS.LVKYPLLLKEILRHTPKDHTDIKPLEEALLV
Retrocopy LLDQKKQDARVQDFLQRCLESPFSRKLDLWSFLDIPRSHLVKYPLLLKEILRHTPKDHTDIKPLEEALLV

Parental  IQGVLSDINLKKGESECQYYIDKLEYLDDKQKDPRIEASKVLLCHGELKNKNGHKLYIFLFQDILVLTRP
          IQGVLSDINLKKGESECQYYIDKLEYLDDKQKDPRIEASKVLLCHGELKNKNGHKLYIFLFQDILVLTRP
Retrocopy IQGVLSDINLKKGESECQYYIDKLEYLDDKQKDPRIEASKVLLCHGELKNKNGHKLYIFLFQDILVLTRP

Parental  VIRNERHSYQVYRQPIPVKELVLEDLQDGDVRMGGSFRGAFSNSDKAKNIFRVRFRDPSPGQSHTLQAND
          VIRNERHSYQVYRQPIPVKELVLEDLQDGDVRMGGSFRGAFSNSDKAKNIFRVRFRDPSPGQSHTLQAND
Retrocopy VIRNERHSYQVYRQPIPVKELVLEDLQDGDVRMGGSFRGAFSNSDKAKNIFRVRFRDPSPGQSHTLQAND

Parental  VFHKQQWFNCIRTAIAPFHQTTSPTEFKGLSELNKGSEKNNPLASHIKSQRKSSTLSGLIPLEVDENSPE
          VFHKQQWFNCIRTAIAPFHQTTSPTEFKGLSELNKGSEKNNPLASHIKSQRKSSTLSGLIPLEVDENSPE
Retrocopy VFHKQQWFNCIRTAIAPFHQTTSPTEFKGLSELNKGSEKNNPLASHIKSQRKSSTLSGLIPLEVDENSPE

Parental  CIPSIAINENSTDIKAHRIQPGSPKAQEKAQLNDKRKETLV
          CIPSIAINENSTDIKAHRIQPGSPKAQEKAQLNDKRKETLV
Retrocopy CIPSIAINENSTDIKAHRIQPGSPKAQEKAQLNDKRKETLV

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_21 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_21 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010007	1 retrocopy	retro_chof_1896,
Monodelphis domestica	ENSMODG00000018500	2 retrocopies	retro_mdom_21 , retro_mdom_239,
Mus musculus	ENSMUSG00000021215	1 retrocopy	retro_mmus_1144,