RetrogeneDB ID: retro_mdom_1633

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:263417712..263419029(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000009117
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017396
• Aliases: None
• Description: None

Sequence

>retro_mdom_1633
ATGACCTGCTCTCTAGACTCCTCTGTTGGTTTTGATGCCTCCGGGCCTGAGCAGACTAAAATCACAGCTCTCCTACCTAA
AGACAGTGATCCAGTCTCATCCTGGGGTAGATTTGGACAGGATGATGATGGACTAGATGACTCCTTACTGGAGCTTTCTG
AGGGAGAGGAGGATGATGGTCACTTCAGTTACACAGAAGAAGAGATTCAGGAGCTGTTGAAGGATGATGACTCACTAAAT
GAACAGTCTCTGGGAGGATTAAGAAAAGATACAGGTGGTCAAGCTGAGAAGTTGGAGAACTATAGTTGTATTTCATTTGA
CTCTCCTCAAGATATAAATGTACTCTGTAGCACAGGACCCAGGGCTGGGCCAGCTAGCATCCATAATCTACCTCAGAAAA
ATATACCAGCTAGGCATGCACCCATTCCAACCAAATCACCTAGCAGACACTTTGTATCAGAAAAAAATCTCTTGAAAATA
ACTCTTGTCCCACCATTTAATACAACAGTTTGTGATGCATTTGGTCCAAAAGAGACTGAGTCTTCTTCAAAAGATGGTTC
CAGTAATGCAAACTGTTTGGGAACTCCCTCCTCCTTGGAGAAAGATGTGAATAGAGAAGGTCATGGCCAGAATGATGGCA
AACTTTGCACTAAAGAAATTAGCTCTGCTTGTTCTGTTTGGAAAGGGACTCCACCTCCTAAAGCTGGCCCTCCACAGGGG
CCTCCTAGAGCAAATACACCTATTTGTGAGGAGTCCGTACCTGTAGCTTCTCCGACCTTGGGACCGACTCCTAGACCAGA
TGTGGCACTGTCTTCAGGCAATGATGGACACAAATTAGGTGACACAGCTAGGTCTCCAGCTGTACAGTCTTCATCTACCA
AACCGGTCAAACTAGACAAGGATTCTAAAAAGAAGGAAGGGTATGAGAGAAGATTAGGGAAAGTCATTCCACTTCAACTG
GCCAAAGCAAGGAGTAAGATTCAGACATTCTCGAAGACTGAGCTGGAACAGAAGAAGCAAATTTATCTTAAGAATGTCAT
TGCTCACTTAAAAAACCCTCTGGAATCTAACCAAGGTGCCTTAGGTGAGTTATGTGCCTTGATGGACCAAGTTGCTAATG
GGGAATATCAAAAGCAGAACCAGCGGTGGCAGCACCCATCAGACCTCACCATGAGAAATTATCCCCGATTCAGACAGAAG
CCCTTACAGAGGTACAGCCTGACTCAGTGGGTAGACAGGAACCTTCGCAGCCATCGTCGGTTCCAAGGCCTTGGTGATCA
ATTCCAACACACTCCAGTTGTTTCATCCCCCCACCTA

Alignment

ORF - retro_mdom_1633 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  MTCSLDSSVGFDASGPEQTKITALLPKDSDPVSSWGRFGQDDDGLDDSLLELSEGEEDDGHFSYTEEEIQ
          MTCSLDSSVGFDASGPEQTKITALLPKDSDPVSSWGRFGQDDDGLDDSLLELSEGEEDDGHFSYTEEEIQ
Retrocopy MTCSLDSSVGFDASGPEQTKITALLPKDSDPVSSWGRFGQDDDGLDDSLLELSEGEEDDGHFSYTEEEIQ

Parental  ELLKDDDSLNEQSLGGLRKDTGGQAEKLENYSCISFDSPQDINVLCSTGPRAGPASIHNLPQKNIPARHA
          ELLKDDDSLNEQSLGGLRKDTGGQAEKLENYSCISFDSPQDINVLCSTGPRAGPASIHNLPQKNIPARHA
Retrocopy ELLKDDDSLNEQSLGGLRKDTGGQAEKLENYSCISFDSPQDINVLCSTGPRAGPASIHNLPQKNIPARHA

Parental  PIPTKSPSRHFVSEKNLLKITLVPPFNTTVCDAFGPKETESSSKDGSSNANCLGTPSSLEKDVNREGHGQ
          PIPTKSPSRHFVSEKNLLKITLVPPFNTTVCDAFGPKETESSSKDGSSNANCLGTPSSLEKDVNREGHGQ
Retrocopy PIPTKSPSRHFVSEKNLLKITLVPPFNTTVCDAFGPKETESSSKDGSSNANCLGTPSSLEKDVNREGHGQ

Parental  NDGKLCTKEISSACSVWKGTPPPKAGPPQGPPRANTPICEESVPVASPTLGPTPRPDVALSSGNDGHKLG
          NDGKLCTKEISSACSVWKGTPPPKAGPPQGPPRANTPICEESVPVASPTLGPTPRPDVALSSGNDGHKLG
Retrocopy NDGKLCTKEISSACSVWKGTPPPKAGPPQGPPRANTPICEESVPVASPTLGPTPRPDVALSSGNDGHKLG

Parental  DTARSPAVQSSSTKPVKLDKDSKKKEGYERRLGKVIPLQLAKARSKIQTFSKTELEQKKQIYLKNVIAHL
          DTARSPAVQSSSTKPVKLDKDSKKKEGYERRLGKVIPLQLAKARSKIQTFSKTELEQKKQIYLKNVIAHL
Retrocopy DTARSPAVQSSSTKPVKLDKDSKKKEGYERRLGKVIPLQLAKARSKIQTFSKTELEQKKQIYLKNVIAHL

Parental  KNPLESNQGALGELCALMDQVANGEYQKQNQRWQHPSDLTMRNYPRFRQKPLQRYSLTQWVDRNLRSHRR
          KNPLESNQGALGELCALMDQVANGEYQKQNQRWQHPSDLTMRNYPRFRQKPLQRYSLTQWVDRNLRSHRR
Retrocopy KNPLESNQGALGELCALMDQVANGEYQKQNQRWQHPSDLTMRNYPRFRQKPLQRYSLTQWVDRNLRSHRR

Parental  FQGLGDQFQHTPVVSSPHL
          FQGLGDQFQHTPVVSSPHL
Retrocopy FQGLGDQFQHTPVVSSPHL

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_1633 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1633 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000537	1 retrocopy	retro_dnov_1346,
Erinaceus europaeus	ENSEEUG00000006053	1 retrocopy	retro_eeur_439,
Myotis lucifugus	ENSMLUG00000000764	1 retrocopy	retro_mluc_1691,
Monodelphis domestica	ENSMODG00000017396	2 retrocopies	retro_mdom_1633 , retro_mdom_62,
Tursiops truncatus	ENSTTRG00000014993	1 retrocopy	retro_ttru_89,