RetrogeneDB ID: retro_mdom_129

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:247713986..247715360(+)
• Located in intron of: ENSMODG00000024111

Retrocopy information

• Ensembl ID: ENSMODG00000008724
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_mdom_129
ATGGAGGTCAAAGAATTGATTGAAAACCTCAAGGCAGAACTCACTTGCCCCATCTGTCTGGACTACTTTACAGACCCAGT
GACTACCAAATGTGGGCATAATTTTTGCAAAGACTGTCTCTTCCAGTGCAATGAGCAAACTGATGCTACACTAACTTGTC
CTGAGTGCAGAGATGTCATTAGATACAGTGATATTTTGCTCAACGACAAAAACCTACAGAATTTGTCCATCACTGGCAAA
ACTCTGAGACAGAAGTTATTGCTGAGCACGGTACTTCTGACCACCTGTGATCAACATGGAGAAAAAGAAAAGATCTTTTG
TGAACAAGACCAAAAACTAATTTGTGGTTCCTGTTTATTAACCCAAGAGCACAAGGATCACCAAGACCTTCCTTTGCAAA
TGGCTGTTGACAAGTGCAAGAAGAAACTTCAGGAGACACTGAATGTGTTACAGGAAAAGGAGGAAGAATTGAAAGAGGAA
ATCAACAAAATGGGAAAAACAGAGGCATATCTTAAGAAGGATACAGACTTTTATAAAGAGTTAATTAAATGTGAATACCA
AAAAATGCACGAGTTCTTATGGGATGAAGAAAATAGACACCTGCAAAAACTGGACCAGGAAATAGAATACAAACTGGCAA
AAGTTGAAACAAATAAGGCCAAACTGTCCCAACAAATTCACTACGTGCAACGAAAGATATTACAAATAGAGGAGAGTTTG
TACGAGGCACCTTTGAAAATGCTCCAGGATATGAAAGACAACTTAGAAAGGAATGAAGAGGTGCTACGTCAACAAACAGA
GACTATTAACCTCACTTATACAACTTACCAGATGAGTGGTTTAATAGAAATTCTCAGGAACTATCAAACAGGTATCACAC
TGGATCCTGAAACAGACAGTTTTCATCTTATCGTGCCAGAACATTTTAAGAGTTTAAAGTACAAGCTTGACCCACCCAAC
CAGCCTGACAAAGAAGAAAGACTTGACTATTTTGTTATTATGTTGGGGACTGAGACCTTTACCGGTGGCAAACATTACTG
GGAAGTAGATGTGGAAGGTCAGACAGAGTGGGTACTTGGAATCTGTGAGGATTCAGTCAGCAAAAATGAGAATCTCTCCA
TGTTATCTGAAGATGTAAGAGCCATAATAGGCTCAAAAGTTAAAAATCAAACACTTTTCTGGAGTTCAAAAGATTGCTTT
TATTCGATACTTCAATATAAAGTGGGCATTTTCCTTAACTATGATGAGGGCAGCATTACTTTTTATGATGTTAATGAAAA
AATTGTTCTCATTAGTTTCCTAAATTCAACTTTTCAAGGGCCCGTTCGCCCTTTCTTCTCCACTTCTCTTGTTAATAAAG
GAAGGACCTCTTAA

Alignment

ORF - retro_mdom_129 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.1 %
• Parental protein coverage: 98.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAKELIESLKAELTCSICLGYFTDPVTALKCGHTFCKDCLLQCDEQADATLTCPECRAVIRYSDIVPNE
          ME.KELIE.LKAELTC.ICL.YFTDPVT..KCGH.FCKDCL.QC.EQ.DATLTCPECR.VIRYSDI..N.
Retrocopy MEVKELIENLKAELTCPICLDYFTDPVTT-KCGHNFCKDCLFQCNEQTDATLTCPECRDVIRYSDILLND

Parental  -NLQNLSITGKTLRQHLLLSPALLTTCDQHGKKEKLFCEQDQKPICDSCLLTQEHKDHQDLPLQMAADKC
          .NLQNLSITGKTLRQ.LLLS..LLTTCDQHG.KEK.FCEQDQK.IC.SCLLTQEHKDHQDLPLQMA.DKC
Retrocopy KNLQNLSITGKTLRQKLLLSTVLLTTCDQHGEKEKIFCEQDQKLICGSCLLTQEHKDHQDLPLQMAVDKC

Parental  KKNLQETLNVLQQKEEELKAEINNILKEEKYFKKDSDFYKELIRCEYRKMHEILYNEENRHLQKLDQEIE
          KK.LQETLNVLQ.KEEELK.EIN...K.E.Y.KKD.DFYKELI.CEY.KMHE.L..EENRHLQKLDQEIE
Retrocopy KKKLQETLNVLQEKEEELKEEINKMGKTEAYLKKDTDFYKELIKCEYQKMHEFLWDEENRHLQKLDQEIE

Parental  DKLAKVEANKAKLSQQIQHVQQKILEIEESLDEAPLEMLQDMKGILERNEELQLQDTETVKLTYTTYQVT
          .KLAKVE.NKAKLSQQI..VQ.KIL.IEESL.EAPL.MLQDMK..LERNEE...Q.TET..LTYTTYQ..
Retrocopy YKLAKVETNKAKLSQQIHYVQRKILQIEESLYEAPLKMLQDMKDNLERNEEVLRQQTETINLTYTTYQMS

Parental  GLIEILRSYQTGITVDPETDRLHLIVPEHFKSLKYRLDPRNQPENEERLDYFVIMLGTETFTSGQHYWEV
          GLIEILR.YQTGIT.DPETD..HLIVPEHFKSLKY.LDP.NQP..EERLDYFVIMLGTETFT.G.HYWEV
Retrocopy GLIEILRNYQTGITLDPETDSFHLIVPEHFKSLKYKLDPPNQPDKEERLDYFVIMLGTETFTGGKHYWEV

Parental  DVEGQTEWVLGICEDSVSKNENLSMLSEDVKAIIGSKVKNQTLFWSSEGCFCSTPPCKLGIFLDYDEGNI
          DVEGQTEWVLGICEDSVSKNENLSMLSEDV.AIIGSKVKNQTLFWSS..CF.S....K.GIFL.YDEG.I
Retrocopy DVEGQTEWVLGICEDSVSKNENLSMLSEDVRAIIGSKVKNQTLFWSSKDCFYSILQYKVGIFLNYDEGSI

Parental  TFYDVNEKTVLISFLNSPFQGPVRPFYSTSLVNKGSSS
          TFYDVNEK.VLISFLNS.FQGPVRPF.STSLVNKG..S
Retrocopy TFYDVNEKIVLISFLNSTFQGPVRPFFSTSLVNKGRTS

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_129 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_129 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,