RetrogeneDB ID: retro_mdom_118

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:285304870..285306355(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023905
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020549
• Aliases: None
• Description: UDP-glucose 6-dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F7AQE4]

Sequence

>retro_mdom_118
ATGTTTGAAATTAAGAAGATCTGTTGCATTGGAGCAGGTTATGTTGGAGGACCCACGTGTAGTGTCATTGCACACATGTG
CCCTGAAATTAGGGTCACAGTTGTTGATGTTAACGAATCTAGAATCAATGCATGGAATTCGGCCACACTCCCAATTTATG
AGCCAGGACTAAAAGAAGTGGTTGAATCTTGTCGGGGAACGAATCTCTTTTTTTCTACCGATATTGATGCTGCCATCAAA
GAGGCTGATCTTGTGTTTATTTCTGTTAATACACCAACAAAAACTTACGGAATGGGAAAAGGTCGTGCAGCAGATCTGAA
GTATATTGAAGCTTGTGCTAGACGGATTGTACAGAACTCAAATGGGTACAAAATTGTGACTGAGAAAAGCACTGTCCCAG
TTAGAGCAGCAGAAAGTATACGGAGGATATTTGATGCAAACACAAAACCCAACTTGAACTTACAGGTGCTCTCCAACCCT
GAATTCTTAGCAGAGGGCACAGCAATCAAAGACCTAAAGAACCCTGACTGGGTACTAATTGGTGGCGATGAAACCCCAGA
GGGACAGAAAGCTGTCTGTGCCCTGTCTGCTGTATATGAACACTGGGTCCCCAAAGAAAAGATCCTCACAACCAATACTT
GGTCTTCAGAGCTTTCTAAATTGGCAGCTAATGCTTTTCTTGCCCAGAGAATCAGTAGCATTAATTCTATCAGTGCCCTG
TGTGAAGCAACAGGAGCTGATGTAGAAGAGGTTGCAACGGCCATTGGGATGGACCAGAGAATTGGAAATAAGTTCCTGAA
GGCCACTGTTGGCTTTGGTGGGAGCTGTTTTCAGAAAGATGTTTTAAATTTAGTTTATCTCTGTGAAGCTCTGAATTTGC
CTGAAGTAGCACGTTATTGGCAGCAGGTAATAGACATGAATGACTACCAGAGAAGGAGGTTTGCATCTCGGATTATTGAT
AGTCTGTTTAATACGGTTACTGATAAGAAGATAGCTATTTTGGGATTTGCATTCAAAAAGGACACTGGAGACACAAGAGA
ATCCTCTAGTATCTACATAAGCAAATACTTGATGGATGAAGGGGCACATCTCCATATTTATGATCCTAAAGTACCAAGGG
AACAAATAGTTGTAGATCTCTCTCATCCTGGTGTTTCAGAGGATGACCAAGTGTCCCGATTGGTGACCATCACAAAGGAT
CCATATGAAGCATGCGATGGAGCCCATGCTGTTGTCATTTGTACTGAATGGGATGTGTTTAAGGAATTGGATTATGAACG
TATTCATAAAAAAATGTTGAAACCAGCCTTTATCTTTGATGGTCGACGTGTCCTAGATGACCTTCACAGTGAATTGCAAA
CCATTGGCTTCCAGATTGAAACAATTGGCAAAAAGGTATCTTCAAAGAGAATTCCATATGCGCCTTCTTCTGAAATTCCA
AAGTTTAGTCTACAGGACCCGCCAAATAAGAAGCCAAGAGTATAA

Alignment

ORF - retro_mdom_118 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFEIKKICCIGAGYVGGPTCSVIAHMCPEIRVTVVDVNESRINAWNSATLPIYEPGLKEVVESCRGTNLF
          MFEIKKICCIGAGYVGGPTCSVIAHMCPEIRVTVVDVNESRINAWNSATLPIYEPGLKEVVESCRGTNLF
Retrocopy MFEIKKICCIGAGYVGGPTCSVIAHMCPEIRVTVVDVNESRINAWNSATLPIYEPGLKEVVESCRGTNLF

Parental  FSTDIDAAIKEADLVFISVNTPTKTYGMGKGRAADLKYIEACARRIVQNSNGYKIVTEKSTVPVRAAESI
          FSTDIDAAIKEADLVFISVNTPTKTYGMGKGRAADLKYIEACARRIVQNSNGYKIVTEKSTVPVRAAESI
Retrocopy FSTDIDAAIKEADLVFISVNTPTKTYGMGKGRAADLKYIEACARRIVQNSNGYKIVTEKSTVPVRAAESI

Parental  RRIFDANTKPNLNLQVLSNPEFLAEGTAIKDLKNPDRVLIGGDETPEGQKAVRALSAVYEHWVPKEKILT
          RRIFDANTKPNLNLQVLSNPEFLAEGTAIKDLKNPD.VLIGGDETPEGQKAV.ALSAVYEHWVPKEKILT
Retrocopy RRIFDANTKPNLNLQVLSNPEFLAEGTAIKDLKNPDWVLIGGDETPEGQKAVCALSAVYEHWVPKEKILT

Parental  TNTWSSELSKLAANAFLAQRISSINSISALCEATGADVEEVATAIGMDQRIGNKFLKASVGFGGSCFQKD
          TNTWSSELSKLAANAFLAQRISSINSISALCEATGADVEEVATAIGMDQRIGNKFLKA.VGFGGSCFQKD
Retrocopy TNTWSSELSKLAANAFLAQRISSINSISALCEATGADVEEVATAIGMDQRIGNKFLKATVGFGGSCFQKD

Parental  VLNLVYLCEALNLPEVARYWQQVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESSS
          VLNLVYLCEALNLPEVARYWQQVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESSS
Retrocopy VLNLVYLCEALNLPEVARYWQQVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESSS

Parental  IYISKYLMDEGAHLHIYDPKVPREQIVVDLSHPGVSEDDQVSRLVTITKDPYEACDGAHAVVICTEWDVF
          IYISKYLMDEGAHLHIYDPKVPREQIVVDLSHPGVSEDDQVSRLVTITKDPYEACDGAHAVVICTEWDVF
Retrocopy IYISKYLMDEGAHLHIYDPKVPREQIVVDLSHPGVSEDDQVSRLVTITKDPYEACDGAHAVVICTEWDVF

Parental  KELDYERIHKKMLKPAFIFDGRRVLDDLHSELQTIGFQIETIGKKVSSKRIPYAPSSEIPKFSLQDPPNK
          KELDYERIHKKMLKPAFIFDGRRVLDDLHSELQTIGFQIETIGKKVSSKRIPYAPSSEIPKFSLQDPPNK
Retrocopy KELDYERIHKKMLKPAFIFDGRRVLDDLHSELQTIGFQIETIGKKVSSKRIPYAPSSEIPKFSLQDPPNK

Parental  KPRV
          KPRV
Retrocopy KPRV

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	0.36 RPM	0.00 RPM
SRP007412_cerebellum	0.33 RPM	0.00 RPM
SRP007412_heart	0.60 RPM	0.00 RPM
SRP007412_kidney	6.58 RPM	0.00 RPM
SRP007412_liver	9.06 RPM	0.00 RPM
SRP007412_testis	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_118 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_118 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008890	1 retrocopy	retro_chof_2472,
Monodelphis domestica	ENSMODG00000020549	1 retrocopy	retro_mdom_118 ,
Otolemur garnettii	ENSOGAG00000004941	1 retrocopy	retro_ogar_1145,