RetrogeneDB ID: retro_mdom_954

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:18703420..18703927(+)
• Located in intron of: ENSMODG00000019520

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GSTA4
• Ensembl ID: ENSMODG00000018810
• Aliases: None
• Description: glutathione S-transferase alpha 4 [Source:HGNC Symbol;Acc:4629]

Sequence

>retro_mdom_954
ATGTCAGATAAACCCTTCCTCCACTACGTTAATGGAAGGGGCAGAATGGAATTCATCTGATGGCTTTTAGCCACAGCTGG
AGTGGAGTTTGAGGAAAAATTTTTTGACACAAAAGAACAACTACAAAAGCTAAAGGAAGACATGTTGCTGTTCCAACAAG
TGCCAATGGTTGAAATCGACGGGATGAAGCTAGTTCAGACAAGAGCCATTCTCCACTACATTGCCAAGAAATGCAATCTT
CTTGGGAATAACCTGAAGGACAGAGCTCTTATTATCATGTATGCAGAAGGAACAATGGATCTGATGGAACTGCTCATAAT
CCATCCCTTCTTAAAACCAGAAGAGCAAAAGCAAAAACTTATTGAAATTGGCAACAAAGCCAAAAACAGATATTTCCTTG
CTTATGAAAAGGTTTTAAGGACTCATGGACAAAACTTTCTTGTTGGTAACCAGATTAGCTTGGCAGATGTGCAACTGATT
GAAGCCATTTTAATGGTGGAAGAGAGA

Alignment

ORF - retro_mdom_954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.49 %
• Parental protein coverage: 76.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDKPILHYFNGRGRMESIRWLLATAGVEFEEKFFDTKEQLQKLKEDKLLFQQVPMVEIDGMKLVQTRAI
          MSDKP.LHY.NGRGRME.I.WLLATAGVEFEEKFFDTKEQLQKLKED.LLFQQVPMVEIDGMKLVQTRAI
Retrocopy MSDKPFLHYVNGRGRMEFI*WLLATAGVEFEEKFFDTKEQLQKLKEDMLLFQQVPMVEIDGMKLVQTRAI

Parental  LHYIAEKYNLLGNNLKDRALIIMYAEGTMDLMELLIIYPFLKPEEQKQKLIEIDNKAKTRYFLAYEKVLR
          LHYIA.K.NLLGNNLKDRALIIMYAEGTMDLMELLII.PFLKPEEQKQKLIEI.NKAK.RYFLAYEKVLR
Retrocopy LHYIAKKCNLLGNNLKDRALIIMYAEGTMDLMELLIIHPFLKPEEQKQKLIEIGNKAKNRYFLAYEKVLR

Parental  THGQNFLVGNQMSLADVQLIEAILMVEER
          THGQNFLVGNQ.SLADVQLIEAILMVEER
Retrocopy THGQNFLVGNQISLADVQLIEAILMVEER

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_954 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_954 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005658	1 retrocopy	retro_amel_787,
Bos taurus	ENSBTAG00000004288	1 retrocopy	retro_btau_670,
Canis familiaris	ENSCAFG00000024066	1 retrocopy	retro_cfam_1440,
Felis catus	ENSFCAG00000005237	1 retrocopy	retro_fcat_1199,
Monodelphis domestica	ENSMODG00000018810	1 retrocopy	retro_mdom_954 ,
Mustela putorius furo	ENSMPUG00000008911	1 retrocopy	retro_mputfur_1383,
Sorex araneus	ENSSARG00000009989	1 retrocopy	retro_sara_769,