RetrogeneDB ID: retro_mdom_1009

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:202891042..202891945(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002633
• Aliases: None
• Description: None

Sequence

>retro_mdom_1009
AGAAAAATACAGAAACTCTACCTAATTGTACATAGGCTTTGGAAGAAATCAAAATACAATAAAAAATTAAGAGAGCCTGA
AGACAACTGGGAAAAGAACTTAAAAAGCAAGATAACTCATTTGGGAAAAGAGGCACTTGAATTAAAGTGAGAAAATAGTG
TCTTGAAAGGCAAAATTAACCAGCTTGAAAATGAGGCAAAGGAGATGAAAGATGACCTCCAAGGAAAATCAGAACAGAAG
GAGAAGGATGACCAAAAAGCCAGGGATGAAATTCAGTCTTTAAAAACTAGAATCCAACAGCTAGAAGCAAATGACTTCAC
AAGGCAATGGGAAACTATAAAACAAAACCAAAAGAATGAAAATTTTGAGAAAAATATGAAAAACCTCATCGACAAAATGG
AAGATCTGGAAAACAGGTTGAGGAGAAACAACTTAAGAATCAGTGGCCTAATTGAAGAACATGACAAAAGAAAAAGTCTG
GATATCATCCTACAGGAAATTATCTATAAAAACTGCCCTAACATTCTAGAGCAGCAGGGAAAAGTGAAGATTGAAAGAAT
CCAAAATCATGTCCCATACTTAATCCCCAAATTCAAAAACTACAAGAGCAAGGAAAAAATATTTCAATCTGCTAAAAAGA
AGTCATTTGGATATAATGGAATCACAGTGACAATAACACAGAATTTGGCTGCATATACAGTGAACAACCAAAAGGCATGG
AATATGATATTCCAGAAAGCAAATGAACTAGGTCTACAATCTAAAATCAACTACCCAGCAAAAATCACTATATTCTTAAA
GGGGAAGGTATGGTCATTTAATAAAATACAAGACTTTCAAGCATTTGTAAAGAAAAGACCAGATCTGAAGAGAAAATTTG
ATGCTAAACACTGAAATCAAAAG

Alignment

ORF - retro_mdom_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.48 %
• Parental protein coverage: 89.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKMETLWLEKWEQIKKEVFNLTNKISQLEKQLEASNIREDQTEKQKQSLKTRIKQ--LEDKQEKHEKVNT
          .K...L.L......KK...N...K....E...E..N.....T...K..L........L..K....E....
Retrocopy RKIQKLYLIVHRLWKKSKYN--KKLREPEDNWE-KNLKSKITHLGKEALELK*ENSVLKGKINQLENEAK

Parental  KHRETEKRISDQKEKDDEKARDEIQSFKTRIQQLEASDFTRHQHTIKQNQKNKIIEENMKHLIHKTEDLE
          .........S.QKEKDD.KARDEIQS.KTRIQQLEA.DFTR....................LI.K.EDLE
Retrocopy EMKDDLQGKSEQKEKDDQKARDEIQSLKTRIQQLEANDFTRQWXXXXXXXXXXXXXXXXXXLIDKMEDLE

Parental  NRSRRDNLRIIGLLEDYDKRKSLDIILQEIIQENCPDITEQEGKVEIERIHRSTHRNVLAKFKKSQTKEK
          NR.RR.NLRI.GL.E..DKRKSLDIILQEII..NCP.I.EQ.GKV.IERI..........KFK....KEK
Retrocopy NRLRRNNLRISGLIEEHDKRKSLDIILQEIIYKNCPNILEQQGKVKIERIQNHV-PYLIPKFKNYKSKEK

Parental  ILQVDKKKSFRKHGTIVRITQDLTASTLKDLQAWNMIFWKARELGLQPRIIYTAKLTIFLQGKVWSFNKI
          I.Q..KKKSF...G..V.ITQ.L.A.T.....AWNMIF.KA.ELGLQ..I.Y.AK.TIFL.GKVWSFNKI
Retrocopy IFQSAKKKSFGYNGITVTITQNLAAYTVNNQKAWNMIFQKANELGLQSKINYPAKITIFLKGKVWSFNKI

Parental  EDFQAFVKKRPDMNRKFDAEAQNSR
          .DFQAFVKKRPD..RKFDA...N..
Retrocopy QDFQAFVKKRPDLKRKFDAKH*NQK

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_1009 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1009 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 1 parental gene, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002633	6 retrocopies	retro_mdom_1009 , retro_mdom_1362, retro_mdom_1477, retro_mdom_1723, retro_mdom_1764, retro_mdom_329,