RetrogeneDB ID: retro_mdom_172

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:159971188..159972283(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000028702
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000000956
• Aliases: None
• Description: None

Sequence

>retro_mdom_172
ATGAACCTGGCCAGTCAGAGCGGGGAGGCCGGCTCCAGCCAGCTGCTCTTCGCCAACTTCAACCAGGACAACACATCCTT
AGCTGTTGGGAGTAAATCTGGTTATAAATTCTTCTCCCTTTCCTCTGTGGATAAGCTGGAACAGATTTATGAATGTACTG
ATACAGAAGATGTGTGTATTGTGGAAAGATTATTTTCAAGTAGCCTGGTGGCCATTGTTAGCCTCAAAGCTCCACGAAAG
CTAAAAGTCTGCCACTTTAAGAAGGGGACTGAAATATGTAATTATAGCTATTCCAATACCATATTGGCAGTCAAATTGAA
TAGACAGAGGTTGATAGTATGCCTAGAAGAATGTCTTTACATACACAATATTCGTGATATGAAGGTACTGCATACAATCA
GGGAAACTCCCCCAAACCCTGCAGGTTTGTGTGCACTGTCAATAAACAATGACAATTGTTACCTGGCTTATCCTGGGAGT
GCAACTATTGGAGAAGTACAAGTCTTTGACACCATTAATTTGAGGGCTGCTAATATGATACCAGCTCATGATAGTCCCCT
AGCAGCTTTGGCTTTTGATGCAAGTGGTACCAAACTTGCCACAGCTTCTGAGAAGGGTACTGTTATTAGGGTATTTTCCA
TTCCAGAAGGACAGAAAATCTTTGAGTTCCGGAGAGGAGTGAAGAGGTGTGTAAGCATCTGCTCTTTGGCCTTCAGTATG
GATGGAATGTTCCTCTCTGCTTCCAGTAACACTGAAACAGTGCACATCTTCAAACTTGAGACTGTGAAAGAGAAACCTCA
GGAGGAACCAACTACCTGGACTGGTTACTTTGGGAAAGTTCTTATGGCCTCTACCAGCTATTTGCCCTCTCAAGTAACAG
AAATGTTTAACCAGGGAAGGGCATTTGCTACTGTCCGACTACCATTCTGCGGTCACAAAAATATCTGTTCACTTGCCACA
ATTCAGAAGATTCCCCGATTATTAGTAGGAGCTTCTGATGGTTACTTATATATGTACAACCTGGATCCTCAGGAAGGAGG
GGAATGTACCCTGATGAAACAACACAACCTTTTCAAAGAAATAGAGGAGGAATAA

Alignment

ORF - retro_mdom_172 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.52 %
• Parental protein coverage: 74.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLAVGSKSGYKFFSLSSVDKLEQIYECTDTEDVCIVERLFSSSLVAIVSLKAPRKLKVCHFKKGTEICNY
          SLAVGSKSGYKFFSLSSVDKLEQIYECTDTEDVCIVERLFSSSLVAIVSLKAPRKLKVCHFKKGTEICNY
Retrocopy SLAVGSKSGYKFFSLSSVDKLEQIYECTDTEDVCIVERLFSSSLVAIVSLKAPRKLKVCHFKKGTEICNY

Parental  SYSNTILAVKLNRQRLIVCLEECLYIHNIRDMKVLHTIRETPPNPAGLCALSINNDNCYLAYPGSATIGE
          SYSNTILAVKLNRQRLIVCLEECLYIHNIRDMKVLHTIRETPPNPAGLCALSINNDNCYLAYPGSATIGE
Retrocopy SYSNTILAVKLNRQRLIVCLEECLYIHNIRDMKVLHTIRETPPNPAGLCALSINNDNCYLAYPGSATIGE

Parental  VQVFDTINLRAANMIPAHDSPLAALAFDASGTKLATASEKGTVIRVFSIPEGQKIFEFRRGVKRCVSICS
          VQVFDTINLRAANMIPAHDSPLAALAFDASGTKLATASEKGTVIRVFSIPEGQKIFEFRRGVKRCVSICS
Retrocopy VQVFDTINLRAANMIPAHDSPLAALAFDASGTKLATASEKGTVIRVFSIPEGQKIFEFRRGVKRCVSICS

Parental  LAFSMDGMFLSASSNTETVHIFKLETVKEKPQEEPTTWTGYFGKVLMASTSYLPSQVTEMFNQGRAFATV
          LAFSMDGMFLSASSNTETVHIFKLETVKEKPQEEPTTWTGYFGKVLMASTSYLPSQVTEMFNQGRAFATV
Retrocopy LAFSMDGMFLSASSNTETVHIFKLETVKEKPQEEPTTWTGYFGKVLMASTSYLPSQVTEMFNQGRAFATV

Parental  RLPFCGHKNICSLATIQKIPRLLVGASDGYLYMYNLDPQEGGECTLMKQHKLDGSME
          RLPFCGHKNICSLATIQKIPRLLVGASDGYLYMYNLDPQEGGECTLMKQH.L....E
Retrocopy RLPFCGHKNICSLATIQKIPRLLVGASDGYLYMYNLDPQEGGECTLMKQHNLFKEIE

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_172 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_172 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000003785	1 retrocopy	retro_csav_7,
Monodelphis domestica	ENSMODG00000000956	1 retrocopy	retro_mdom_172 ,