RetrogeneDB ID: retro_mdom_1431

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:17362643..17363380(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADSS
• Ensembl ID: ENSMODG00000006559
• Aliases: None
• Description: adenylosuccinate synthase [Source:HGNC Symbol;Acc:292]

Sequence

>retro_mdom_1431
CCAGTTGTGACAGCCATGTTGCTTGCTGAGATTGTCCATGACATGGCCTTGGTGCCCAATGGAGAATACGGAATTTCCTT
GGTTCAGTTAGGAGGAAACCAAGTGACAGTGGTGCTAGACACACAGTGAGGCAATGAGGGCAAGGGGAAGGTGGTGGATG
TGTTGGCGCAGGAAGCCAACATCATCTGCTGCTGCCAGGGAGGAAACAGTGCTGGCCATTCAGTTGTTGTGGATTCTGTA
GAATATGACTTTCATCTCTTACCAAGTGGGATCATCACTCCAAATGTCACTGCATTCATTGGAAATGGTGTAATTCACCT
GCCAGGATTATTTGAAGAAGCAGAGAAAAATGTTCAAAAGGGAAAGGCCTCAAAGGCTGGGAAAAGAGGCTTATAATTTC
TGACAGAGCTCATATTATATTTGACTTCCACCAAGCAGCAGATAGCATTCAGGAATAACAGAGGCAAGAGCAAGCTGGAA
AGAATTTGGGCACCACAAAAAAAGGTATTGGCCCAGTTTATTCCTCCAAAACTTCTCGAAGTGGACCCAGGATATGTGAT
CTTGTTTTAGACTTTGAAGGCTTCTCTGAGAGGTTCAAAGTTTTAGCTAATCAATGTAAACCTATATATCCCACTTTGGA
AATTGTTATTGAAGGCAAATTACAAAAACTCAAAGACTATATGGAAAGGATTAAACCAATGGTGAGAGATGGGTTTTATT
TTCTCTCTGAAGCCCTC

Alignment

ORF - retro_mdom_1431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.26 %
• Parental protein coverage: 51.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVPPAMSLAEAGLAVASVPNGECGSSLARSGGNRVTVVLGAQWGDEGKGKVVDLLAQDADIVCRCQGGNN
          PV..AM.LAE.....A.VPNGE.G.SL...GGN.VTVVL..Q.G.EGKGKVVD.LAQ.A.I.C.CQGGN.
Retrocopy PVVTAMLLAEIVHDMALVPNGEYGISLVQLGGNQVTVVLDTQ*GNEGKGKVVDVLAQEANIICCCQGGNS

Parental  AGHTVVVDSVEYDFHLLPSGIINPNVTAFIGNGVVIHLPGLFEEAEKNVQKGK-GLEGWEKRLIISDRAH
          AGH.VVVDSVEYDFHLLPSGII.PNVTAFIGNGV.IHLPGLFEEAEKNVQKGK.GL.GWEKRLIISDRAH
Retrocopy AGHSVVVDSVEYDFHLLPSGIITPNVTAFIGNGV-IHLPGLFEEAEKNVQKGK<GLKGWEKRLIISDRAH

Parental  IVFDFHQAADGIQEQQRQEQAGKNLGTTKKGIGPVYSSKASRSGLRMCDLVSDFEGFSERFKVLANQYKS
          I.FDFHQAAD.IQE.QRQEQAGKNLGTTKKGIGPVYSSK.SRSG.R.CDLV.DFEGFSERFKVLANQ.K.
Retrocopy IIFDFHQAADSIQE*QRQEQAGKNLGTTKKGIGPVYSSKTSRSGPRICDLVLDFEGFSERFKVLANQCKP

Parental  IYPTLEIDIEGELQKLKGYMERIKPMVRDGVYFLYEAL
          IYPTLEI.IEG.LQKLK.YMERIKPMVRDG.YFL.EAL
Retrocopy IYPTLEIVIEGKLQKLKDYMERIKPMVRDGFYFLSEAL

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_1431 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1431 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015815	1 retrocopy	retro_cfam_322,
Callithrix jacchus	ENSCJAG00000017069	2 retrocopies	retro_cjac_2721, retro_cjac_452,
Homo sapiens	ENSG00000035687	1 retrocopy	retro_hsap_1826,
Myotis lucifugus	ENSMLUG00000017320	1 retrocopy	retro_mluc_1435,
Monodelphis domestica	ENSMODG00000006559	1 retrocopy	retro_mdom_1431 ,
Mustela putorius furo	ENSMPUG00000015741	1 retrocopy	retro_mputfur_1286,
Oryctolagus cuniculus	ENSOCUG00000013982	1 retrocopy	retro_ocun_458,
Pongo abelii	ENSPPYG00000000057	1 retrocopy	retro_pabe_1496,
Pan troglodytes	ENSPTRG00000002178	1 retrocopy	retro_ptro_1167,