RetrogeneDB ID: retro_mdom_1530

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:137682555..137683160(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GL1
• Ensembl ID: ENSMODG00000000931
• Aliases: None
• Description: SH3-domain GRB2-like 1 [Source:HGNC Symbol;Acc:10830]

Sequence

>retro_mdom_1530
CTCCAGAACCCCTGTGAGAAAGATTTAAAAGAGATCCTGCATCTTCTGAAAAAGCTGGAGGGCAAGCTTTTGGACAGTGA
CTATAAGGAGAAGCATCAGGGAAAGATGCTAGAGCTTCATCCAATGATAGAGAAATATGAAGAGTCCAAGGCTGTGGCAG
AGACCAGTATATACAATTTGGAGACCGACATTGAACAGGTGAGCCAGCTCTCAGCCCTGGTGGATGCACAACTGGGTTAC
CACATGTAAGCACTCCAGATCCTGGCTAAGCTGGCAGACATGCTCAAGTACAGGGTTTGGGAAGCCTCTTCTTGTCCCAG
GTGGGTATACAAACCAAAGTCTAGAGATTCCAGTGACTTTGGAGAGTCTGACCACTCCAATGGACATATTTCTTGTGCCC
CAGACCCCAAGATGACAGCTTCTTCCTCTTTCTGATACTCTGATATACCCATCTGGACCCCTGTTAGGAGCATGCCACCT
CCTGACCAATCCAGCTGCAAGGCCCTATATGACTTGAGCCAGATAATGGTGTGGATTTAGACTTCTGCAAGGGTGACATC
ATCACACTGGCCAACCAATCAACCAATCAGATTGATGAAAAATGG

Alignment

ORF - retro_mdom_1530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.96 %
• Parental protein coverage: 54.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQNLCDKDLKEIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQAMEKFEESKEVAETSMHNLLETDIEQV
          LQN.C.KDLKEI.H.LKKLEG..LD.DYK.K.QGK....EL....EK.EESK.VAETS..N.LETDIEQV
Retrocopy LQNPCEKDLKEILHLLKKLEGKLLDSDYKEKHQGKML--ELHPMIEKYEESKAVAETSIYN-LETDIEQV

Parental  SQLSALVDAQLDYHRQAVQILDELADKLKRRMREASSRPKREYKPKPRDSYDFGEPDQSNGGFPCAPAPK
          SQLSALVDAQL.YH..A.QIL..LAD.LK.R..EASS.P...YKPK.RDS.DFGE.D.SNG...CAP.PK
Retrocopy SQLSALVDAQLGYHM*ALQILAKLADMLKYRVWEASSCPRWVYKPKSRDSSDFGESDHSNGHISCAPDPK

Parental  ITASSSFRSSDKPIRTPIRSMPPLDQPSCKALYD-FEPENDGELGFREGDIITL----TNQIDENW
          .TASSSF..SD.PI.TP.RSMPP.DQ.SCKALYD..EP.N...L.F..GDIITL....TNQIDE.W
Retrocopy MTASSSF*YSDIPIWTPVRSMPPPDQSSCKALYD<LEPDNGVDLDFCKGDIITLANQSTNQIDEKW

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_1530 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1530 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000141985	3 retrocopies	retro_hsap_1742, retro_hsap_1745, retro_hsap_1859,
Gorilla gorilla	ENSGGOG00000008198	3 retrocopies	retro_ggor_2151, retro_ggor_2258, retro_ggor_675,
Macaca mulatta	ENSMMUG00000000273	1 retrocopy	retro_mmul_1264,
Monodelphis domestica	ENSMODG00000000931	1 retrocopy	retro_mdom_1530 ,
Monodelphis domestica	ENSMODG00000008125	1 retrocopy	retro_mdom_821,
Nomascus leucogenys	ENSNLEG00000003122	2 retrocopies	retro_nleu_2914, retro_nleu_3075,
Pongo abelii	ENSPPYG00000009405	6 retrocopies	retro_pabe_1488, retro_pabe_1516, retro_pabe_1530, retro_pabe_1542, retro_pabe_1700, retro_pabe_3542,