RetrogeneDB ID: retro_mdom_512

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:111527395..111528405(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GXYLT1
• Ensembl ID: ENSMODG00000008913
• Aliases: None
• Description: glucoside xylosyltransferase 1 [Source:HGNC Symbol;Acc:27482]

Sequence

>retro_mdom_512
AGGTATAGACTGACAAAAATACAAACTGCTGAGACAATATACCTAGCTGTGGTAGCCTGTGGTGAACGACTGGAAGAGAC
TATAACCATGATAAAATCAGCTATTATTTTCAGCATCCAACCTCTTCAGTTCCACATTTTTGCTGAAGACCAATTGCACC
ATAGCTTCAAAAAAATACTTGATGGCTGGAAATTTCTGCAAACATTTAATTACACTACATATCCAATAACTTTTCCAACC
AAGAATGCAGCAGAATGGAAAAAACTCTTTAAACCATGTGCTTCACAAAGATTGTTTTTGCGATTAATCCTGAAAGAAGT
TGACTCACTATTGTATGTTGACACCAATATTCTTTTTTTACGCCCTGTTGATGATATTTGGTCACTCCTAAAAAAACTTA
ACTCTACACAAATTGCTGCATGGCACCAGAACATGAGGAACCTCGGATTGGTTGGAATAATCGCTTGCCAGACATCCATA
CTATGGAAAAACTGGAATAAATTCTGGAGTTATGTTAATGAACATGACATGAATAAGAAGAAAATATTTCAAGAATGACA
TGACAACTGCACATCTACAGTGGGGAGAGATATTTATGCCATTACTTAAAAAATACAAACTTAATATCACATGGGGTGAT
CAAGATTTATTAAATATAATGTTTTTTCATAATCCAGAAAGCCTTTTTGTTTTTCCATGCCACTGGAATCATCAGCCTGA
TCATTGTGTCTATGGAAGTAATTGCCAAGAAGCTGAAGAAGAAGGAATCTTTATTCTTCATGGGAACAGAGATGTTTACC
ATGATGATAAGCAGCCAGTTTTTAGAGCCATTTAGGAAGCACTGCAAAATTGCTCTTTTGGAGATGATAAGCTACATTCT
TTGTTACACCCATTAGAACTGGAACTACAAAAGACTGTACATACATACTGTGGGAGAATGCACAAGATATTCACAAAAAC
AACTAACAAAAAGTATAAAAGATAGTTATGACCGACCATCAAAAGAAAGG

Alignment

ORF - retro_mdom_512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.53 %
• Parental protein coverage: 75.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RYRLTKIQTAETMHLAVVACGERLEETITMIKSAIIFSIQPLQFHIFAEDQLHHSFKKILDGWKFLQTFN
          RYRLTKIQTAET..LAVVACGERLEETITMIKSAIIFSIQPLQFHIFAEDQLHHSFKKILDGWKFLQTFN
Retrocopy RYRLTKIQTAETIYLAVVACGERLEETITMIKSAIIFSIQPLQFHIFAEDQLHHSFKKILDGWKFLQTFN

Parental  YTTYPITFPTENAAEWKKLFKPCASQRLFLPLILKEVDSLLYVDTDILFLRPVDDIWSLLKKFNSTQIAA
          YTTYPITFPT.NAAEWKKLFKPCASQRLFL.LILKEVDSLLYVDT.ILFLRPVDDIWSLLKK.NSTQIAA
Retrocopy YTTYPITFPTKNAAEWKKLFKPCASQRLFLRLILKEVDSLLYVDTNILFLRPVDDIWSLLKKLNSTQIAA

Parental  -MAPEHEEPRIGWYNRF-ARHPYYGKTGINSGVMLMNMTRIRRKYFKNDMTTAHLQWGEILMPLLKKYKL
          .MAPEHEEPRIGW.NR..ARHPYYGKTGINSGVMLMNMT.IRRKYFKNDMTTAHLQWGEI.MPLLKKYKL
Retrocopy <MAPEHEEPRIGWNNRL<ARHPYYGKTGINSGVMLMNMT*IRRKYFKNDMTTAHLQWGEIFMPLLKKYKL

Parental  NITWGDQDLLNIMFFHNPESLFVFPCHWNYRPDHCIYGSNCREAEEEGIFILHGNRGVYHDDKQPVFRAI
          NITWGDQDLLNIMFFHNPESLFVFPCHWN..PDHC.YGSNC.EAEEEGIFILHGNR.VYHDDKQPVFRAI
Retrocopy NITWGDQDLLNIMFFHNPESLFVFPCHWNHQPDHCVYGSNCQEAEEEGIFILHGNRDVYHDDKQPVFRAI

Parental  YEALRNCSFGDDKLQSLLHPLELELQKTVHTYCGRMHKIFT-KQLTKSIRDSYDRPSKER
          .EAL.NCSFGDDKL.SLLHPLELELQKTVHTYCGRMHKIFT.KQLTKSI.DSYDRPSKER
Retrocopy *EALQNCSFGDDKLHSLLHPLELELQKTVHTYCGRMHKIFT>KQLTKSIKDSYDRPSKER

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	0.20 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.59 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_512 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_512 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 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151233	5 retrocopies	retro_hsap_2295, retro_hsap_4167, retro_hsap_4177, retro_hsap_4258, retro_hsap_4267,
Gorilla gorilla	ENSGGOG00000027928	3 retrocopies	retro_ggor_1702, retro_ggor_1950, retro_ggor_2798,
Monodelphis domestica	ENSMODG00000008913	1 retrocopy	retro_mdom_512 ,
Mus musculus	ENSMUSG00000036197	1 retrocopy	retro_mmus_2325,
Nomascus leucogenys	ENSNLEG00000017947	1 retrocopy	retro_nleu_2700,
Pongo abelii	ENSPPYG00000004419	2 retrocopies	retro_pabe_1849, retro_pabe_1976,
Pan troglodytes	ENSPTRG00000004836	5 retrocopies	retro_ptro_1623, retro_ptro_2832, retro_ptro_2960, retro_ptro_3006, retro_ptro_848,
Rattus norvegicus	ENSRNOG00000005234	1 retrocopy	retro_rnor_2754,