RetrogeneDB ID: retro_mdom_1836

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:42851346..42852372(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000022818
• Aliases: None
• Description: None

Sequence

>retro_mdom_1836
AGGCTTAGGAACATGGAGCCCAAAGGTTTAATCGAGAACTTCAAAGGTGATCTCACTTGCTCCATCTGTCTGGGCTACTT
CAGCAAACCAGGGACTGTCAAATATGGGTACAGTTTTGCAGAAAGTGTCTCCTCCAGTGCAGTGAGGAATCTGATGGTAC
ATTAATCTATCCAGAGTGCAGAGGAATCATTAGATACAGTTATATCATGCCCAACAAGAACCTGCAGAATCTATCCATCA
CTGGCAAAACTCTCTGACCAAATTTACTGCTGAGCACAGTACTTCTGACTATCTGTGATCAAAATGGGGAAAAGAGAAGC
TATTTTGTGAGGAAGAGGAAAAACTAATTTGAGGTTCCTACTTAGTAACCCAAGAGCACAAGGATCACCAAGTCCTTTCC
TTGCAAATGGCTGACAAGTGAAAGGAGAAACTCAGGAGACATTGAATTTCTTACAAGAAAAAGTGGAGAAATTTAAAATT
GCATTGAACAATGTGAGAATGAAAGAGGCACAACATAAGGAGAAATTTTGTGTTCTTAAACAATCAATTATGTGTGAATA
TGGTAAAATGCACCAGTTCATATGGGATGAAGAATATCAATACCTGAACAGCCTGGAGCAAGATTCAGAAGACAACCTGG
CAAATTTCAACAAAAATGAGGCTAAATTGACCCAACAAATCCAACATCTGCAACAAATGATATTATAAATAGAGGATAAT
TTGGAGAAGGCACCCTTGGAAATGCTCCAGGTTATGAAAGCCACCTTGAAAAAGGATGAGAAACTGCTAGTTCAAGAACC
AGAGGTTGTTTCCATTGAGTGGACCAGCACTTCATCACTGGTTTAAGAGAAAAGCTCTTGACCTTTTACGGGGATATTTC
TCTAAAACATGAAACATCCTATCTTTCTCTCATTCTGCCTGAAATTTTAAAAAATGCCAAGAATGGACATGCCCCCAGAA
GACCAGGCTGACCAGGAAGAAAGACTTGATTATGTTATTAATGTATTGGGAACTCAGATAGTCACT

Alignment

ORF - retro_mdom_1836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.71 %
• Parental protein coverage: 74.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RLRNMEAKELIESLKAELTCSICLGYFTDPVTALKCGHTF-CKDCLLQCDEQADATLTCPECRAVIRYSD
          RLRNME.K.LIE..K..LTCSICLGYF..P.T..K.G..F.C..CLLQC.E..D.TL..PECR..IRYS.
Retrocopy RLRNMEPKGLIENFKGDLTCSICLGYFSKPGT-VKYGYSF<CRKCLLQCSEESDGTLIYPECRGIIRYSY

Parental  IVPNENLQNLSITGKTLRQHLLLSPALLTTCDQHGKK-EKLFCEQDQKPICDSCLLTQEHKDHQDLPLQM
          I.PN.NLQNLSITGKTL...LLLS..LLT.CDQ.G.K.EKLFCE...K.I..S.L.TQEHKDHQ.L.LQM
Retrocopy IMPNKNLQNLSITGKTL*PNLLLSTVLLTICDQNGEK<EKLFCEEEEKLI*GSYLVTQEHKDHQVLSLQM

Parental  AADKCKKNL-QETLNVLQQKEEELKAEINNILKEEKYFKKDSDFYKELIRCEYRKMHEILYNEENRHLQK
          A.DK.K..L.QETLN.LQ.K.E..K...NN....E...K......K..I.CEY.KMH.....EE...L..
Retrocopy A-DK*KEKL<QETLNFLQEKVEKFKIALNNVRMKEAQHKEKFCVLKQSIMCEYGKMHQFIWDEEYQYLNS

Parental  LDQEIEDKLAKVEANKAKLSQQIQHVQQKILEIEESLDEAPLEMLQDMKGILERNEELQLQDTETVKLTY
          L.Q..ED.LA....N.AKL.QQIQH.QQ.IL.IE..L..APLEMLQ.MK..L...E.L..Q..E.V....
Retrocopy LEQDSEDNLANFNKNEAKLTQQIQHLQQMIL*IEDNLEKAPLEMLQVMKATLKKDEKLLVQEPEVVSIEW

Parental  TT-YQVTGLIEILRSYQTGITVDPETDRLHLIVPEHFKSLK-YRLDPRNQPENEERLDYFVIMLGTETFT
          T.....TGL.E.L......I....ET..L.LI.PE..K..K.....P..Q...EERLDY....LGT...T
Retrocopy TS<HFITGLREKLLTFYGDISLKHETSYLSLILPEILKNAK>MDMPPEDQADQEERLDYVINVLGTQIVT

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_1836 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1836 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001670	1 retrocopy	retro_mdom_60,
Monodelphis domestica	ENSMODG00000022818	2 retrocopies	retro_mdom_129, retro_mdom_1836 ,
Tursiops truncatus	ENSTTRG00000012631	1 retrocopy	retro_ttru_81,