RetrogeneDB ID: retro_mdom_2

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:46911952..46913161(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025204
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000014339
• Aliases: None
• Description: None

Sequence

>retro_mdom_2
ATGGCAAACGAATCCAAATGGCGCGGAGAATCGAAAAGAATCAAGACGGTCTCTCTGGTGCCGATTGCGCAGGCGATCGA
AAGAAGTAGGCGCGATCGGGAGGAGCGGCAGAAAATAGTCCTGTGGAAGAAGCCGTTAACTACCTTGCGGTACTTCTTAC
TAGAAACTGTGATTAACTTGAAGGTCTGGGCCTATAGAGTATGGTGGTGGCGAAGCATCTTGCTGTTAACTCTTCTGCTA
TTGATCTCCGCCGGGACTGTCTGTTACATCGAAGGACCTCACCAGCTGTATGTGAGTTACTTAGAGAAAAAGATACTGTG
GTGTAGCTACTGGGTTGGTCTAGGAATTTTGTCCTCTGTTGGCCTTGGCACTGGTCTCCATACTTTTCTGCTCTACCTGG
GCCCTCACATTGCTTCTGTTACCCTGGCTGCTTATGAGTGCAACACTGTTAACTTCCCAGAGCCACCCTATCCTGAAAGG
ATTACCTGCCCAGATGAAGCTATCCAGGAAGAGTTTATTTCTTTATGGGCCATTCTGTCAAAGGTTAGGCTTGAAGCCTG
TATGTGGGGTGCGGGCACAGCCATTGGAGAACTGCCCCCTTACTTTATGGCCAGGGCTGCCCGATTGTCAGAGCTTGAAC
CTGATGATGAGGATTATGAGGAGATTGAAGAGATGTTGGAAGATCCCGATTCTCCCCAAGACTTTGCTTCTTGGGCTAAG
AAAGCTATACAGACCCTGGTGAAAAAGGTTGGATTTTTTGGAATATTGGCCTGTGCTTCAATTCCCAACCCTCTATTTGA
TCTGGCAGGGATAGCATGTGGACATTTCCTGGTTCCCTTTTGGACCTTTTTTGGTGCAACCCTCATCGGAAAGGCTATAG
TGAAGATGCACATTCAGAAACTCCTTGTTATTATGGCCTTCAGCAAACACATTGTAGAACAGATGGTGACTCTCATTGGT
GCTATCCCCACTTTAGGCCCTTCTCTCCAGAAACCATTCCAAGAATACTTTGAGGCGCAGCGCCTAAAGCTTCATCACAA
ATCTGAGATGAAGAACATAATGGAGAAAGAAAACTGGGTGTCCTGGGTGTTTGAAAAGCTGGTTGTTGTGATGGTGGCCT
ATTTCGTATTATCTATAATCAATTCCATGGCCCAGAGTTATGCCAGACGAATCCAGCAGCAAATGAACTCAGGAGAAAAA
ATGAATTAA

Alignment

ORF - retro_mdom_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.3 %
• Parental protein coverage: 97.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQRLTGMNKEQHNGNFTDPSSLNEKKRRDREERQNIVLWRQPLITLQYFFLEILINLKEWTIKLWHRRNI
          E....G..K..............E..RRDREERQ.IVLW..PL.TL.YF.LE..INLK.W....W..R.I
Retrocopy ESKWRGESKRIKTVSLVPIAQAIERSRRDREERQKIVLWKKPLTTLRYFLLETVINLKVWAYRVWWWRSI

Parental  VVSFLVLLAVLTAMYYIEGTHQQYVRYMEKKIFWCAYWVGLGILSSVGLGTGLHTFLLYLGPHIASVTLA
          ....L.LL.......YIEG.HQ.YV.Y.EKKI.WC.YWVGLGILSSVGLGTGLHTFLLYLGPHIASVTLA
Retrocopy LLLTLLLLISAGTVCYIEGPHQLYVSYLEKKILWCSYWVGLGILSSVGLGTGLHTFLLYLGPHIASVTLA

Parental  AYECNSVNFPEPPYPDQIICPDEEGIEGSISLWTIISKVRLEACMWGAGTAIGELPPYFMARAARLSGAE
          AYECN.VNFPEPPYP..I.CPDE...E..ISLW.I.SKVRLEACMWGAGTAIGELPPYFMARAARLS..E
Retrocopy AYECNTVNFPEPPYPERITCPDEAIQEEFISLWAILSKVRLEACMWGAGTAIGELPPYFMARAARLSELE

Parental  PDDEEYQEFEEMLEHAESAQDFASRAKLAVQNMVQKVGFFGILACASIPNPLFDLAGITCGHFLVPFWTF
          PDDE.Y.E.EEMLE...S.QDFAS.AK.A.Q..V.KVGFFGILACASIPNPLFDLAGI.CGHFLVPFWTF
Retrocopy PDDEDYEEIEEMLEDPDSPQDFASWAKKAIQTLVKKVGFFGILACASIPNPLFDLAGIACGHFLVPFWTF

Parental  FGATLIGKAIVKMHIQKLFVIITFSKHIVEQMVALIGAVPSLGPSLQKPFQEYLEAQRQKLHHKSE-EGM
          FGATLIGKAIVKMHIQKL.VI..FSKHIVEQMV.LIGA.P.LGPSLQKPFQEY.EAQR.KLHHKSE....
Retrocopy FGATLIGKAIVKMHIQKLLVIMAFSKHIVEQMVTLIGAIPTLGPSLQKPFQEYFEAQRLKLHHKSEMKNI

Parental  PQGENWLSWMFEKLVIVMVCYFILSIINSMAQSYAKRIQQQMYSEEK
          ...ENW.SW.FEKLV.VMV.YF.LSIINSMAQSYA.RIQQQM.S.EK
Retrocopy MEKENWVSWVFEKLVVVMVAYFVLSIINSMAQSYARRIQQQMNSGEK

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_2 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000014339	1 retrocopy	retro_mdom_2 ,
Mus musculus	ENSMUSG00000018171	1 retrocopy	retro_mmus_2640,
Nomascus leucogenys	ENSNLEG00000000724	1 retrocopy	retro_nleu_818,
Rattus norvegicus	ENSRNOG00000003967	1 retrocopy	retro_rnor_527,
Sarcophilus harrisii	ENSSHAG00000016264	1 retrocopy	retro_shar_52,
Drosophila melanogaster	FBgn0052675	1 retrocopy	retro_dmel_49,