RetrogeneDB ID: retro_mdom_1121

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:161810290..161811904(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024985
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000021477
• Aliases: None
• Description: None

Sequence

>retro_mdom_1121
ATGGGGTGCATTAAAAGTAAGGGAGACAAAGATCCAGCTATGAAATATAGAACCGAAAGCAGTTCAGAGCCCATTAGCAT
AAATGTCGGTCATTTTGGATCAGAACTTACCCTAGGGTGCCAGTCATCTTCAATAAAGGGATCAACTGTTAATTTTTCCA
GTCATTCCATGGCACTATTTGGAAGTTCAGCAGGGATGACACCTTTTGGAGGTGCTACTTCTTCCTTTTCATCTATGCCA
AGTCAACATTCTACTGGTCTAACAGGTGGTGTCACTATATTCGTGGCTTTATATGATTATGAAGCTAGAACTACAGAAGA
TCTTTCTTTTAAGAAGAGTGAAAGATTTCAAATAATTAATAATACAGAAGGAGACTGGTGGGAAGCAAGATCCATAGCTA
CAGGAAAGACTGGATATATCCCTAGCAATTATGTAGCTCCTGCCGACTCCATTCAGGCAGAAGAGTGGTATTTTGGCAAA
ATGGGCAGAAAAGATGCTGAGAGCCTACTTCTCAATCCTGGGAACCAACGAGGTATCTTCTTAGTAAGAGAAAGTGAAAC
CACCAAAGGTGCTTTTCCCCTTTCTATTTGTGATTGAGATGAGATAAGGGGTGACAATGTTAAACACTACAAAATTCGGA
AACTTGACAATGGTGGATACTATATCACAACCAGAGCACAATTTGATACTTTACAGAAACTAGTCAAACACTACACAGAA
CATGCTGATGGTTTGTGCCATAAGTTAACAACTGTGTGTCCCATTGTGAAACCTCAGACTCAAGGTTTGGCAAAAGATGC
TTGGGAAATTCCTCGAGAATCTTTACGTCTAGAAGTTAAACTAGAACAAGGATGTTTTGGTGAAGTATGGATGGGAACAT
GGAATGGGATGACAAAGGTAGCAATCAAAACACTAAAGCCTGGTACAATGATGCCGGAAGCTTTTCTTCAGGAAGCTCAG
ATCATGAAGAAACTAAGACTTGTTCCATTATATGCTGTTGTTTCTGAGGAACCAATTTATATTGTCACTGAATTTATGTC
AAAAGGAAGCTTATTAGATTTCCTTAAGGAAGGAGATGGAAAGAATTTGAAGCTCCCCCAACTGGTTGATATGGCAGTAC
AGATTGCTGATGGTATGACATATATCGAAAGAATGAACTACATCCACTGAGATCTTCGAGCGGCTAACATCCTTGTAGGA
GATAATCTTGTTTGTAAAATAGCAGATTTTGGATTAGCCAGGCTAATTGAAGATAATGAATACACTGCAAGGCAAGGAGC
CAAATTTCCAATCAAGTGGACAGCTCCTGAGGCTGCATTGTATGGTCATTTCACAATTAAATCTGATGTTTGGTCATTTG
GAATTCTGCTAACAGAACTTGTAACAAAGCGTAGAGTGCCATATCCAGGGATGGTAAATCATGAAGTCTTGGAACAGGTA
GAATGGGGATACAGAATGCCTTGTCCTCAGGGCTGTCCAGAATCTCTCCATGAGCTGATGAACCTTTGTTGGAAGAAGGA
CCCTGATGAAAGACCAACATTTGAATATATTCAGTCCTTCTTAGAAGACTACTTTACTGCTACAGAACCACAGTACCAGC
CAGGTGACAATTTA

Alignment

ORF - retro_mdom_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGCVKSKEDKDPAMKYGTESSSEPISINVGHFGSELTLGCQSSSIKGSTVNFSSHSMAPFGGSAGMTPFG
          MGC.KSK.DKDPAMKY.TESSSEPISINVGHFGSELTLGCQSSSIKGSTVNFSSHSMA.FG.SAGMTPFG
Retrocopy MGCIKSKGDKDPAMKYRTESSSEPISINVGHFGSELTLGCQSSSIKGSTVNFSSHSMALFGSSAGMTPFG

Parental  GATSSFSSMPSPHSTGLTGGVTIFVALYDYEARTTEDLSFKKSERFQIINNTEGDWWEARSIATGKTGYI
          GATSSFSSMPS.HSTGLTGGVTIFVALYDYEARTTEDLSFKKSERFQIINNTEGDWWEARSIATGKTGYI
Retrocopy GATSSFSSMPSQHSTGLTGGVTIFVALYDYEARTTEDLSFKKSERFQIINNTEGDWWEARSIATGKTGYI

Parental  PSNYVAPADSIQAEEWYFGKMGRKDAERLLLNPGNQRGIFLVRESETTKGAFSLSIRDWDEIRGDNVKHY
          PSNYVAPADSIQAEEWYFGKMGRKDAE.LLLNPGNQRGIFLVRESETTKGAF.LSI.D.DEIRGDNVKHY
Retrocopy PSNYVAPADSIQAEEWYFGKMGRKDAESLLLNPGNQRGIFLVRESETTKGAFPLSICD*DEIRGDNVKHY

Parental  KIRKLDNGGYYITTRAPFDTLQKLVKHYTEHADGLCHKLTTVCPTVKPQTQGLAKDAWEIPRESLRLEVK
          KIRKLDNGGYYITTRA.FDTLQKLVKHYTEHADGLCHKLTTVCP.VKPQTQGLAKDAWEIPRESLRLEVK
Retrocopy KIRKLDNGGYYITTRAQFDTLQKLVKHYTEHADGLCHKLTTVCPIVKPQTQGLAKDAWEIPRESLRLEVK

Parental  LGQGCFGEVWMGTWNGTTKVAIKTLKPGTMMPEAFLQEAQIMKKLRHDKLVPLYAVVSEEPIYIVTEFMS
          L.QGCFGEVWMGTWNG.TKVAIKTLKPGTMMPEAFLQEAQIMKKLR...LVPLYAVVSEEPIYIVTEFMS
Retrocopy LEQGCFGEVWMGTWNGMTKVAIKTLKPGTMMPEAFLQEAQIMKKLR---LVPLYAVVSEEPIYIVTEFMS

Parental  KGILLDFLKEGDGKHLKLPQLVDMAAQIADGMAYIERMNYIHRDLRAANILVGDNLVCKIADFGLARLIE
          KG.LLDFLKEGDGK.LKLPQLVDMA.QIADGM.YIERMNYIH.DLRAANILVGDNLVCKIADFGLARLIE
Retrocopy KGSLLDFLKEGDGKNLKLPQLVDMAVQIADGMTYIERMNYIH*DLRAANILVGDNLVCKIADFGLARLIE

Parental  DNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELVTKGRVPYPGMVNREVLEQVERGYRMP
          DNEYTARQGAKFPIKWTAPEAALYG.FTIKSDVWSFGILLTELVTK.RVPYPGMVN.EVLEQVE.GYRMP
Retrocopy DNEYTARQGAKFPIKWTAPEAALYGHFTIKSDVWSFGILLTELVTKRRVPYPGMVNHEVLEQVEWGYRMP

Parental  CPQGCPESLHELMNLCWKKDPDERPTFEYIQSFLEDYFTATEPQYQPGDNL
          CPQGCPESLHELMNLCWKKDPDERPTFEYIQSFLEDYFTATEPQYQPGDNL
Retrocopy CPQGCPESLHELMNLCWKKDPDERPTFEYIQSFLEDYFTATEPQYQPGDNL

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_1121 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1121 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000176105	1 retrocopy	retro_hsap_2551,
Monodelphis domestica	ENSMODG00000021477	1 retrocopy	retro_mdom_1121 ,
Oryctolagus cuniculus	ENSOCUG00000005874	1 retrocopy	retro_ocun_894,
Otolemur garnettii	ENSOGAG00000003375	1 retrocopy	retro_ogar_1684,
Pan troglodytes	ENSPTRG00000009824	1 retrocopy	retro_ptro_1487,