RetrogeneDB ID: retro_mdom_375

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:311576394..311577176(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000007725
• Aliases: None
• Description: None

Sequence

>retro_mdom_375
ATGGCGCTCAAAAGGAACCACTCAGAGAGTGGAGTGATTGCCAACAATAGAGAATATTCTAATGACCTATGATCATGTGG
AGCTCTCCCTTCAGTGACATGGATCATATGACAGATCCCTTCAATGGAACCAAGAAAGGCAGCCTCTATTTAACTCCTTA
CAGAGTTATTTTTCTGTCCAAGGGGAGAGATTCCATGCAGTCATTCATGATGCCATTTTACCTAATGAAGGACTATGAGA
TCAAGCAGCCTGTGTTTGGTGCAAATTATATCAGGGGAACAGTAAAGGCAAAAGCAAGAGGTGGCTAGGAAGGATCAGTT
GTTTACAAATTGACCTTTGCAGCAGGAGGTGCCATTGAGATTGGACAGCGAATGCTACAGGTGGCCTCCTAAGCTTCCAG
AGGTAAAGTCCCCAATGGAGCTTACAGATACTCTTACATGTCCAATGGAGCTATGCTTTTCCCATGCCAGCTGCCAATGG
AATGTACCCAAACCCTCCAAGCTATCCCTTTGCTCCACCTCCACCCGAGTTTTATCCAGGACCTCCTATGATGGATGGAG
CTATAGGGTAAATACAGCCCCCAACCACCTCCATATCCAGGGCCCATGGAGCCACCTGTTACAGGTGGCCCTGATGTACC
ATCTACTCCTGCAGCTGAAGTAAAAGCTGCTGAAGCTACTGCCAGCACCTACTATAACCCTGTCAATCCCCATAAAGTCT
ACATGCCCATGGACCAGCCCCCACCACCTTTGTACTACCCCCCAGAGGACAAGAAGACCCAG

Alignment

ORF - retro_mdom_375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALNRNHSESGVIVNNT-ENILMTYDHVELS-FSDMDHMTDPFKGTKKGSLYLTPYRVIFLSKGRDSMQS
          MAL.RNHSESG....N..ENILMTYDHVELS.FSDMDHMTDPF.GTKKGSLYLTPYRVIFLSKGRDSMQS
Retrocopy MALKRNHSESG-VIANN>ENILMTYDHVELS>FSDMDHMTDPFNGTKKGSLYLTPYRVIFLSKGRDSMQS

Parental  FMMPFYLMKDYEIKQPVFGANYIRGTVKAEAGGGWEGSAVYKLTFAAGGAIEFGQRMLQVASQASRGEVP
          FMMPFYLMKDYEIKQPVFGANYIRGTVKA.A.GG.EGS.VYKLTFAAGGAIE.GQRMLQVAS.ASRG.VP
Retrocopy FMMPFYLMKDYEIKQPVFGANYIRGTVKAKARGG*EGSVVYKLTFAAGGAIEIGQRMLQVAS*ASRGKVP

Parental  NGAYGYSYMPNGA-YAFPMPAANGMYPNPPSYPYAPPPPEFYPGPPMMDGAIGYMQPP-PPPYPGPMEPP
          NGAY.YSYM.NGA.YAFPMPAANGMYPNPPSYP.APPPPEFYPGPPMMDGAIG..QPP.PPPYPGPMEPP
Retrocopy NGAYRYSYMSNGA<YAFPMPAANGMYPNPPSYPFAPPPPEFYPGPPMMDGAIG*IQPP>PPPYPGPMEPP

Parental  VAGGPDVPSTPAAEAKAAEAAASAYYNPVNPHNVYMPTDQPPPPPYYPPEDKKTQ
          V.GGPDVPSTPAAE.KAAEA.AS.YYNPVNPH.VYMP.DQPPPP.YYPPEDKKTQ
Retrocopy VTGGPDVPSTPAAEVKAAEATASTYYNPVNPHKVYMPMDQPPPPLYYPPEDKKTQ

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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_375 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_375 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004946	1 retrocopy	retro_cfam_1038,
Callithrix jacchus	ENSCJAG00000037619	1 retrocopy	retro_cjac_575,
Felis catus	ENSFCAG00000005760	1 retrocopy	retro_fcat_1454,
Homo sapiens	ENSG00000132471	1 retrocopy	retro_hsap_1926,
Gorilla gorilla	ENSGGOG00000009241	2 retrocopies	retro_ggor_1404, retro_ggor_698,
Macropus eugenii	ENSMEUG00000000070	1 retrocopy	retro_meug_579,
Macaca mulatta	ENSMMUG00000009381	2 retrocopies	retro_mmul_1062, retro_mmul_854,
Monodelphis domestica	ENSMODG00000007725	3 retrocopies	retro_mdom_1410, retro_mdom_1847, retro_mdom_375 ,
Mustela putorius furo	ENSMPUG00000013775	1 retrocopy	retro_mputfur_645,
Nomascus leucogenys	ENSNLEG00000001625	1 retrocopy	retro_nleu_1214,
Ochotona princeps	ENSOPRG00000006045	2 retrocopies	retro_opri_301, retro_opri_851,
Pongo abelii	ENSPPYG00000008640	3 retrocopies	retro_pabe_693, retro_pabe_75, retro_pabe_913,
Pan troglodytes	ENSPTRG00000009660	1 retrocopy	retro_ptro_15,
Ictidomys tridecemlineatus	ENSSTOG00000021421	2 retrocopies	retro_itri_1585, retro_itri_660,