RetrogeneDB ID: retro_mdom_204

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:72990517..72991792(+)
• Located in intron of: ENSMODG00000003748

Retrocopy information

• Ensembl ID: ENSMODG00000024973
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011590
• Aliases: None
• Description: None

Sequence

>retro_mdom_204
CAACTGAGGCGGGAGCAGGGCTCCATGTTTGCCTTTGCCGCTCTGACCCTGGTTCTGCTGGGTGGACCTGGGATCACTGC
CCTGGACAATGGATTAGCTCTGACCCCCACTATGGGCTGGCTGCCCTGGGAGCGCTTCACATGCAATGTGAACTGCATCC
AGGACCCAGAGAACTGCATTAGTGAACAACTCTTTATGCAGATGGCTGATCTCATGGTATCAGAAGGCTGGAAGGATGCG
GGCTATGAGTACGTCTGCATCGATGACTGTTGGTTGGCCTCCAAACGAAATAAAGATGGTACACTCAAGGCAGACCCCAA
ACGCTTCCCGAGTGGAATTCGGCATTTGGCAAATTATGTACACTCCAGGGGGCTGAAGTTGGGCATTTATCAAGATGTAG
GAACTCTCACCTGCGCTGGATACCCAGGAAGCTTTGGCTACTACGATATTGATGCCCAAACCTTTGCCGATTGGGGAGTG
GACCTGCTCAAGTTTGATGGATGTTACTATAAAGACATAGAAAGTTTGGTAGAGGGCTACAAGCACATGTCCATCGCCCT
CAACAAAACTGGCAGAAGTATTCTATATTCCTGTGAGTGGCCTCTATATACGAGACCCTTCCAGGAGCCCAATTACACAG
AAATTCGACAGTATTGCAACCACTGGAGGAACTATGTCGATATCTTGGACTCTTGGAGAAGCGTGAAGAGTATTCTGGCC
TGGACCGCGTCTAAACAGGACAGCCTTGTTCCTGCCGCTGGACCGGGGGGTTGGAACGATCCCGACATGCTAGTGATCGG
CAACTTTGGACTCAGCTGGGATCAACAAGTGACTCAGATGGCCCTGTGGGCTATCATGGCGGCCCCACTCTTCATGTCCA
ATGACCTACGCCACATCAGCTGCCGATCCAAGGCTCTGCTCCAGAATAAAGATGTCATTGCAATCAACCAGGATCCTTTG
GGCAAGCAGGGCTACCTGCTCAGGAAGGACAAGAACTTCGAAGTGTGGGAACGACCCCTGTCGAATTTAGCCTGGGCCGT
GGCTGTGCTAAACCAGAAAGAGATCGGGGGGCCTCAGAATTATGCCTTTTCCACTTCTGCTCTGGGCCAGGGAGTAGGCT
GTGCCCCTGCTTGCTTTATCACCCAGATCCTCCCTGTTAAAGAAGAGCTGGGACTTTATACATGGGTATCTCTGTTGAAG
GTTCAGGTAAACCCCACAGGTACTGTCCTGTTGAAGCTACAGGCTTACCAGCAACACGAATATTCCAGCCATACC

Alignment

ORF - retro_mdom_204 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.05 %
• Parental protein coverage: 91.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QERGPMFAFAALALVLLGGPWATALDNGLALTPTMGWLHWERFTCNVDCIEDPENCISEGLFMQMADIMV
          .E.G.MFAFAAL.LVLLGGP..TALDNGLALTPTMGWL.WERFTCNV.CI.DPENCISE.LFMQMAD.MV
Retrocopy REQGSMFAFAALTLVLLGGPGITALDNGLALTPTMGWLPWERFTCNVNCIQDPENCISEQLFMQMADLMV

Parental  SEGWKDAGYEYVCIDDCWLASKRNKNGSLQADPKRFPSGIRHLADYVHSRGLKLGIYQDVGTLTCAGYPG
          SEGWKDAGYEYVCIDDCWLASKRNK.G.L.ADPKRFPSGIRHLA.YVHSRGLKLGIYQDVGTLTCAGYPG
Retrocopy SEGWKDAGYEYVCIDDCWLASKRNKDGTLKADPKRFPSGIRHLANYVHSRGLKLGIYQDVGTLTCAGYPG

Parental  SFGYYDIDAQTFADWGVDLLKFDGCNFKDVESLVEGYKSMSSALNKTGRSILYSCEWPLYLRPFQEPHYT
          SFGYYDIDAQTFADWGVDLLKFDGC..KD.ESLVEGYK.MS.ALNKTGRSILYSCEWPLY.RPFQEP.YT
Retrocopy SFGYYDIDAQTFADWGVDLLKFDGCYYKDIESLVEGYKHMSIALNKTGRSILYSCEWPLYTRPFQEPNYT

Parental  EIRQYCNHWRNYGDIFDSWNSVKTILAWTASKQESLVPAAGPGGWNDPDMLVIGNFGLSWDQQVTQMALW
          EIRQYCNHWRNY.DI.DSW.SVK.ILAWTASKQ.SLVPAAGPGGWNDPDMLVIGNFGLSWDQQVTQMALW
Retrocopy EIRQYCNHWRNYVDILDSWRSVKSILAWTASKQDSLVPAAGPGGWNDPDMLVIGNFGLSWDQQVTQMALW

Parental  AIMAAPLFMSNDLRHISPQSKNLLQNKDVIAINQDPLGKQGYQLRKDKDFEVWERPLSNLAWAVAVLNQK
          AIMAAPLFMSNDLRHIS..SK.LLQNKDVIAINQDPLGKQGY.LRKDK.FEVWERPLSNLAWAVAVLNQK
Retrocopy AIMAAPLFMSNDLRHISCRSKALLQNKDVIAINQDPLGKQGYLLRKDKNFEVWERPLSNLAWAVAVLNQK

Parental  EIGGPQNYAFSTSALGHGLGCSPACYITQILPVKEDLGLYTWISQLKVRVNPTGTVLLKLQTYQQQEYSS
          EIGGPQNYAFSTSALG.G.GC.PAC.ITQILPVKE.LGLYTW.S.LKV.VNPTGTVLLKLQ.YQQ.EYSS
Retrocopy EIGGPQNYAFSTSALGQGVGCAPACFITQILPVKEELGLYTWVSLLKVQVNPTGTVLLKLQAYQQHEYSS

Parental  HT
          HT
Retrocopy HT

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	24.95 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_204 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_204 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010267	1 retrocopy	retro_chof_1479,
Monodelphis domestica	ENSMODG00000011590	1 retrocopy	retro_mdom_204 ,
Oryctolagus cuniculus	ENSOCUG00000010859	1 retrocopy	retro_ocun_1190,
Ictidomys tridecemlineatus	ENSSTOG00000004771	1 retrocopy	retro_itri_1519,