RetrogeneDB ID: retro_mdom_782

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:467409911..467410334(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRI
• Ensembl ID: ENSMODG00000010355
• Aliases: None
• Description: sorcin [Source:HGNC Symbol;Acc:11292]

Sequence

>retro_mdom_782
TTAACTAACCCTGGTATTGCTGAAGTATATAACCCTTTCAACCTGGAGACTTGCAGGCTTATGGTCTCAATGTTGGATAG
GGATATGTCTGGCGCCATGGGTTTTAGTGAATTTAAGGAACTTTGGACTGTATTGAATGTCTAGAGACAACACTTCATAA
GCTTTGACAGTGCCCAAAGTGGAGCAGTAGATCCCCAAGAATTGCAGAAAGCCCTGGGAACCATGGAATTTACATTGGGT
CCCCAAGCAATGACTTCAATTGCAAAATGATACAGCATCAATGGAAAGATTACCTTCAATGACTATATTGCTTGTTGTGT
AAAACTTAGAGCTCTCACTGATAGTTTTCAAAGAAGGGATGCTGCTCAACAAGGGGTTGGGAATTTCCTGTATCATGATT
TCATACAGTGTATGATGAGGGTC

Alignment

ORF - retro_mdom_782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.56 %
• Parental protein coverage: 60.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTQSGIAGGYKPFNLETCRLMVSMLDRDMSGTMGFSEFKELWAVLNGWRQHFISFDSDRSGTVDPQELQK
          LT..GIA..Y.PFNLETCRLMVSMLDRDMSG.MGFSEFKELW.VLN..RQHFISFDS..SG.VDPQELQK
Retrocopy LTNPGIAEVYNPFNLETCRLMVSMLDRDMSGAMGFSEFKELWTVLNV*RQHFISFDSAQSGAVDPQELQK

Parental  ALGTMGFRLSPQAVTSIAKRYSTNGKITFDDYIACCVKLRALTDSFRRRDTAQQGVVNFPYDDFIQCVMS
          ALGTM.F.L.PQA.TSIAK.YS.NGKITF.DYIACCVKLRALTDSF.RRD.AQQGV.NF.Y.DFIQC.M.
Retrocopy ALGTMEFTLGPQAMTSIAK*YSINGKITFNDYIACCVKLRALTDSFQRRDAAQQGVGNFLYHDFIQCMMR

Parental  V
          V
Retrocopy V

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_782 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_782 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 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001855	1 retrocopy	retro_cfam_498,
Cavia porcellus	ENSCPOG00000010096	1 retrocopy	retro_cpor_216,
Latimeria chalumnae	ENSLACG00000000210	1 retrocopy	retro_lcha_89,
Loxodonta africana	ENSLAFG00000027380	2 retrocopies	retro_lafr_1186, retro_lafr_487,
Monodelphis domestica	ENSMODG00000010355	1 retrocopy	retro_mdom_782 ,
Monodelphis domestica	ENSMODG00000017573	1 retrocopy	retro_mdom_1930,
Mustela putorius furo	ENSMPUG00000018313	1 retrocopy	retro_mputfur_1147,
Pteropus vampyrus	ENSPVAG00000007438	2 retrocopies	retro_pvam_1112, retro_pvam_734,
Rattus norvegicus	ENSRNOG00000049780	1 retrocopy	retro_rnor_1237,
Ictidomys tridecemlineatus	ENSSTOG00000004372	1 retrocopy	retro_itri_607,
Tupaia belangeri	ENSTBEG00000004434	1 retrocopy	retro_tbel_4493,
Tarsius syrichta	ENSTSYG00000014640	1 retrocopy	retro_tsyr_1832,
Xenopus tropicalis	ENSXETG00000008793	1 retrocopy	retro_xtro_25,