RetrogeneDB ID: retro_mdom_94

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:101172450..101173767(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000022505
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020776
• Aliases: None
• Description: None

Sequence

>retro_mdom_94
ATGGAGGGCACCGAGCTGGCCGTGCAGGTCGTGGGTACCTGGCTCACGCTAGTGCTGAGCCTCATCCTGCTACCCTCGGC
GTTCGGCGTGTCGCTAGGCATCTCCGAAATCTACATGAAGATTCTGGTGAAGACTCTGGAGTGGGCCACATTAAGAATTG
AGAAAGGATCTCCAAAGGAATCATCACTTAAAAGCCCATCTTCTGTTGGTATTATCCAGAGAGATGAGTCGCCTATGGAG
AAAGGAATATCTGGACATCGAGGGGGGGACTTTGAACTCTCCGATGTGTTCTATTTCTCCAAAAAGGGATTTGAAGCCAT
TGTGGAAGATGAAGTGACTCAGAGATTCTCCTCAGAGGAGTTAGTGTCTTGGAATCTCCTCACACGAACAAATATTAACT
TCCAGTATATCAGCCTTCGATTAACAACAGTATGGGTGCTGGGAGTTATAGTGCGTTACTGTTTCCTTCTTCCTCTTCGC
ATTACTTTGGCTTTCTTTGGGATTAGTTTGCTGGTTATAGGAACTACTATGGTTGGACAGCTCCCAAATAGCAGTTTGAA
AAACTGGCTAAGTGAACTGGTCCATCTGACTTGCTGCAGAATCTGTGTCCGAGCTCTTTCTGGTACTATTCATTACCATA
ACAAGCAGTACCGACCCCAGAAAGGAGGCATTTGTGTTGCTAATCATACTTCTCCAATAGATGTTCTGATCTTGACGACT
GATGGATGCTATGCCATGGTTGGACAGGTTCATGGCGGACTCATGGGAATCATTCAGAGGGCCATGGTTAAAGCTTGTCC
CCATGTTTGGTTTGAACGTTCAGAAATGAAGGACCGACATCTAGTGACTAAAAGGTTAAGAGAACACATTGCTGATAAGA
AAAAATTGCCCATTTTAATTTTCCCTGAAGGAACCTGTATAAACAACACATCAGTCATGATGTTTAAAAAGGGAAGTTTT
GAAATAGGAGGAACTATATATCCAGTTGCAATAAAGTATAACCCTCAGTTTGGTGATGCCTTTTGGAATAGTAGTAAGTA
CAACATGGTGAACTACTTGCTACGAATGATGACCAGCTGGGCCATAGTCTGTGATGTGTGGTACCTGCCCCCAATGACCA
GAGAGGAAGATGAAGATGCAGTACAGTTTGCAAACAGGGTTAAATCTGCTATTGCTGTGCAAGGAGGATTGACTGAACTT
CCCTGGGACGGAGGTCTGAAGAGAGCCAAGGTCAAAGATACTTTGAAGGAAGAGCAGCAGAAGAACTATAGCAAGATGAT
AGTTGGAAATGGGTCTATAAATACAGAGTCTGAATGA

Alignment

ORF - retro_mdom_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGTELAVQVVGTWLTLVLSLILLPSAFGVSLGISEIYMKILVKTLEWATLRIEKGSPKESSLKSPSSVG
          MEGTELAVQVVGTWLTLVLSLILLPSAFGVSLGISEIYMKILVKTLEWATLRIEKGSPKESSLKSPSSVG
Retrocopy MEGTELAVQVVGTWLTLVLSLILLPSAFGVSLGISEIYMKILVKTLEWATLRIEKGSPKESSLKSPSSVG

Parental  IIQRDESPMEKGISGHRGGDFELSDVFYFSKKGFEAIVEDEVTQRFSSEELVSWNLLTRTNINFQYISLR
          IIQRDESPMEKGISGHRGGDFELSDVFYFSKKGFEAIVEDEVTQRFSSEELVSWNLLTRTNINFQYISLR
Retrocopy IIQRDESPMEKGISGHRGGDFELSDVFYFSKKGFEAIVEDEVTQRFSSEELVSWNLLTRTNINFQYISLR

Parental  LTTVWVLGVIVRYCFLLPLRITLAFFGISLLVIGTTMVGQLPNSSLKNWLSELVHLTCCRICVRALSGTI
          LTTVWVLGVIVRYCFLLPLRITLAFFGISLLVIGTTMVGQLPNSSLKNWLSELVHLTCCRICVRALSGTI
Retrocopy LTTVWVLGVIVRYCFLLPLRITLAFFGISLLVIGTTMVGQLPNSSLKNWLSELVHLTCCRICVRALSGTI

Parental  HYHNKQYRPQKGGICVANHTSPIDVLILTTDGCYAMVGQVHGGLMGIIQRAMVKACPHVWFERSEMKDRH
          HYHNKQYRPQKGGICVANHTSPIDVLILTTDGCYAMVGQVHGGLMGIIQRAMVKACPHVWFERSEMKDRH
Retrocopy HYHNKQYRPQKGGICVANHTSPIDVLILTTDGCYAMVGQVHGGLMGIIQRAMVKACPHVWFERSEMKDRH

Parental  LVTKRLREHIADKKKLPILIFPEGTCINNTSVMMFKKGSFEIGGTIYPVAIKYNPQFGDAFWNSSKYNMV
          LVTKRLREHIADKKKLPILIFPEGTCINNTSVMMFKKGSFEIGGTIYPVAIKYNPQFGDAFWNSSKYNMV
Retrocopy LVTKRLREHIADKKKLPILIFPEGTCINNTSVMMFKKGSFEIGGTIYPVAIKYNPQFGDAFWNSSKYNMV

Parental  NYLLRMMTSWAIVCDVWYLPPMTREEDEDAVQFANRVKSAIAVQGGLTELPWDGGLKRAKVKDTLKEEQQ
          NYLLRMMTSWAIVCDVWYLPPMTREEDEDAVQFANRVKSAIAVQGGLTELPWDGGLKRAKVKDTLKEEQQ
Retrocopy NYLLRMMTSWAIVCDVWYLPPMTREEDEDAVQFANRVKSAIAVQGGLTELPWDGGLKRAKVKDTLKEEQQ

Parental  KNYSKMIVGNGSINTESE
          KNYSKMIVGNGSINTESE
Retrocopy KNYSKMIVGNGSINTESE

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_94 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_94 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
Callithrix jacchus	ENSCJAG00000005314	1 retrocopy	retro_cjac_1176,
Monodelphis domestica	ENSMODG00000020776	1 retrocopy	retro_mdom_94 ,