RetrogeneDB ID: retro_mdom_1333

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:48451852..48452354(-)
• Located in intron of: ENSMODG00000008158

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB4
• Ensembl ID: ENSMODG00000012305
• Aliases: None
• Description: MOB family member 4, phocein [Source:HGNC Symbol;Acc:17261]

Sequence

>retro_mdom_1333
TCCAATATTGACGAAATTCTTGAACCACCTGAAGGCCAAGATGAAGGTATATGGAAATATGAGCATTTAAGGCAATTCTG
CCTGGAGCTAAATGGACTTGTGTCAAACTTCAGAGTGAGTGCCATCCAGATGCATGTACTCAAGTGACAGCAACTGAACA
ATGGGTTTTTCTTTGTGCAGCTCACAAAACTCCAAAAGAGTGTCCTGCTATAGACACACTAGGCACATGCTTGATGGTGC
TGCATGTCTTCTGAATAGCAATAAATATTTTCCGAGCAGAGTTAGCAAAAAGGAGTTATCTGTAGCCAAACTAGGATCAG
TGTGGATTTACAGAATATTTTACATGCTTATTTTCATCATCAGCAAATACGAGAATGAAACTTTTTTATGTCACCGATTT
ACTAAATTTGTGATGAAATATAATTTGATGTCTGAGGATAACCTGATTGTACCAATTTTGGAAGAGGAAATGCACAATTC
AGTATCTGGGGAAAGTGAAGCA

Alignment

ORF - retro_mdom_1333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.52 %
• Parental protein coverage: 77.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SNIDKILEPPEGQDEGVWKYEHLRQFCLELNGLA-VKLQSECHPDTCTQMTATEQWIFLCAAHKTPKECP
          SNID.ILEPPEGQDEG.WKYEHLRQFCLELNGL..VKLQSECHPD.CTQ.TATEQW.FLCAAHKTPKECP
Retrocopy SNIDEILEPPEGQDEGIWKYEHLRQFCLELNGLV<VKLQSECHPDACTQVTATEQWVFLCAAHKTPKECP

Parental  AID-YTRHTLDGAACLLNSNKYFPSRVSIKESSVAKLGSVCRRIYRIFSHAYFHHRQIFDEYENETFLCH
          AID..TRH.LDGAACLLNSNKYFPSRVS.KE.SVAKLGSV...IYRIF....F....I...YENETFLCH
Retrocopy AID<HTRHMLDGAACLLNSNKYFPSRVSKKELSVAKLGSVW--IYRIFYMLIF----IISKYENETFLCH

Parental  RFTKFVMKYNLMSKDNLIVPILEEEVQNSVSGESEA
          RFTKFVMKYNLMS.DNLIVPILEEE..NSVSGESEA
Retrocopy RFTKFVMKYNLMSEDNLIVPILEEEMHNSVSGESEA

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_1333 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1333 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 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004020	2 retrocopies	retro_cjac_1960, retro_cjac_3238,
Cavia porcellus	ENSCPOG00000012746	2 retrocopies	retro_cpor_318, retro_cpor_804,
Echinops telfairi	ENSETEG00000000932	1 retrocopy	retro_etel_952,
Homo sapiens	ENSG00000115540	2 retrocopies	retro_hsap_2275, retro_hsap_906,
Gorilla gorilla	ENSGGOG00000009005	2 retrocopies	retro_ggor_733, retro_ggor_743,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112,
Macaca mulatta	ENSMMUG00000016547	1 retrocopy	retro_mmul_829,
Monodelphis domestica	ENSMODG00000012305	2 retrocopies	retro_mdom_1333 , retro_mdom_963,
Nomascus leucogenys	ENSNLEG00000006881	2 retrocopies	retro_nleu_287, retro_nleu_376,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30,
Otolemur garnettii	ENSOGAG00000000272	1 retrocopy	retro_ogar_2739,
Ochotona princeps	ENSOPRG00000016650	2 retrocopies	retro_opri_444, retro_opri_812,
Pongo abelii	ENSPPYG00000013047	6 retrocopies	retro_pabe_1943, retro_pabe_2021, retro_pabe_3600, retro_pabe_781, retro_pabe_795, retro_pabe_970,
Pan troglodytes	ENSPTRG00000012775	3 retrocopies	retro_ptro_1609, retro_ptro_626, retro_ptro_640,
Sarcophilus harrisii	ENSSHAG00000017821	1 retrocopy	retro_shar_351,
Sus scrofa	ENSSSCG00000016079	2 retrocopies	retro_sscr_804, retro_sscr_824,
Ictidomys tridecemlineatus	ENSSTOG00000021024	1 retrocopy	retro_itri_727,
Tarsius syrichta	ENSTSYG00000001726	1 retrocopy	retro_tsyr_1673,