RetrogeneDB ID: retro_mdom_1332

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:48326190..48326691(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000008113
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C1orf194
• Ensembl ID: ENSMODG00000002197
• Aliases: None
• Description: chromosome 1 open reading frame 194 [Source:HGNC Symbol;Acc:32331]

Sequence

>retro_mdom_1332
ATGTCACTTAATCGAGAGCCCACACAGAAGCCCAAGAACAAAAATGAAGATACCTGCATGAGCAAAAGAGAGTCCCAGAA
ACCCCGCTTCACCAGCCCAACCCCTGTTATCAAGCAGCTCGATCCCTGGAACCGACTCCATGCAACTTCCACAATTGCCC
GTATCAGGGGGAGCGTATATTTCTATAACCCGGACGTTCCCCTGGATGACTTGGATTTCCGAATTACATCCTTGTACAAC
CACCATATGGGATACCTTCAGGACAAGGCACAGACTCTAATCCATGAGGAGACCATCAATGACACCCATGGAGTCATCAA
ATTCCAGGACCCACATGAAATAATATGTCCTTCCTTACCTCCCATCCCTCCCGGAACAATGAGGCAATGGGTCAACCCCA
AGAAGGAATCAATCCACAGTACCAAAGGGTCCATAACATCACCTCATCTACCCACTAGCAATGGTGGCTATTCTCGCAAG
ACTGATGGTGGCTTCTTCTCC

Alignment

ORF - retro_mdom_1332 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.95 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPTRDPLQNPKFENEDSYVGKREGQKLPYMNPPHLIQQQNPWHRLHATTTIASVRRDVYFYDPEIPQDD
          M...R.P.Q.PK..NED....KRE.QK.....P...I.Q..PW.RLHAT.TIA..R..VYFY.P..P.DD
Retrocopy MSLNREPTQKPKNKNEDTCMSKRESQKPRFTSPTPVIKQLDPWNRLHATSTIARIRGSVYFYNPDVPLDD

Parental  LDFRITSLYNHHTGLFQDKAQSLVHHETVYDTHGVVKLQHPDEIVPPTPLPPITTRALMRHWINPKKESI
          LDFRITSLYNHH.G..QDKAQ.L.H.ET..DTHGV.K.Q.P.EI..P..LPPI.....MR.W.NPKKESI
Retrocopy LDFRITSLYNHHMGYLQDKAQTLIHEETINDTHGVIKFQDPHEIICPS-LPPIPP-GTMRQWVNPKKESI

Parental  HSVQGTIVAPHTAATNGGYSRKTDGGFFS
          HS..G.I..PH....NGGYSRKTDGGFFS
Retrocopy HSTKGSITSPHLPTSNGGYSRKTDGGFFS

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_1332 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1332 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019853	3 retrocopies	retro_cfam_1217, retro_cfam_1651, retro_cfam_1827,
Monodelphis domestica	ENSMODG00000002197	1 retrocopy	retro_mdom_1332 ,
Mustela putorius furo	ENSMPUG00000002787	3 retrocopies	retro_mputfur_561, retro_mputfur_568, retro_mputfur_672,