RetrogeneDB ID: retro_mdom_1070

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:500139620..500139923(+)
• Located in intron of: ENSMODG00000023713

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000009520
• Aliases: None
• Description: None

Sequence

>retro_mdom_1070
ATGTTCGCCTGCGCCAAGCTCGTCTGCTCCCTGGCACTGAGCCGTGCTGGATCCAGAATTGTATACTGACCAATTTCTGT
AGCAGTGTTGTCTTGACCAGAGATCAGGACTGGAGAAGGCAACACAGTATCTAATGGGGCCCAGAACGGGGTGTCTCAGC
TAGTACTAAGGGAGTTCCAGACCAGTGCTATCAGCAGAGATACTGCTGCTAAATTTATTGGTGCAGGTACTGCCACAGTA
GGAGTGGCTGGTTCTGGTGCTGGTAGTGGAACTGTCTTTGGTTCTCTCATTATTGGTTATGCC

Alignment

ORF - retro_mdom_1070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.38 %
• Parental protein coverage: 73.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFACAKLACSPALIRAGSRIVYRPISAAVLSRPEVRTGEGNTVSNGAQNRVSQLALREFQTSAISRDVDT
          MFACAKL.CS.AL.RAGSRIVY.PIS.AVLS.PE.RTGEGNTVSNGAQN.VSQL.LREFQTSAISR..DT
Retrocopy MFACAKLVCSLALSRAGSRIVY*PISVAVLS*PEIRTGEGNTVSNGAQNGVSQLVLREFQTSAISR--DT

Parental  AAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYA
          AAKFIGAG.ATVGVAGSGAG.GTVFGSLIIGYA
Retrocopy AAKFIGAGTATVGVAGSGAGSGTVFGSLIIGYA

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_1070 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1070 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 19 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012367	1 retrocopy	retro_amel_1829,
Bos taurus	ENSBTAG00000002944	1 retrocopy	retro_btau_838,
Canis familiaris	ENSCAFG00000013366	2 retrocopies	retro_cfam_4, retro_cfam_5,
Choloepus hoffmanni	ENSCHOG00000012592	3 retrocopies	retro_chof_189, retro_chof_2561, retro_chof_508,
Callithrix jacchus	ENSCJAG00000008207	3 retrocopies	retro_cjac_279, retro_cjac_38, retro_cjac_4183,
Cavia porcellus	ENSCPOG00000006194	1 retrocopy	retro_cpor_479,
Dasypus novemcinctus	ENSDNOG00000010440	2 retrocopies	retro_dnov_235, retro_dnov_396,
Loxodonta africana	ENSLAFG00000010768	1 retrocopy	retro_lafr_120,
Myotis lucifugus	ENSMLUG00000012822	1 retrocopy	retro_mluc_23,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Monodelphis domestica	ENSMODG00000009520	3 retrocopies	retro_mdom_1070 , retro_mdom_295, retro_mdom_545,
Mustela putorius furo	ENSMPUG00000013986	1 retrocopy	retro_mputfur_818,
Oryctolagus cuniculus	ENSOCUG00000012164	1 retrocopy	retro_ocun_949,
Otolemur garnettii	ENSOGAG00000027578	1 retrocopy	retro_ogar_1938,
Rattus norvegicus	ENSRNOG00000001596	1 retrocopy	retro_rnor_1106,
Sorex araneus	ENSSARG00000006733	1 retrocopy	retro_sara_82,
Ictidomys tridecemlineatus	ENSSTOG00000013572	4 retrocopies	retro_itri_1091, retro_itri_1236, retro_itri_324, retro_itri_438,
Tupaia belangeri	ENSTBEG00000012159	1 retrocopy	retro_tbel_54,
Tursiops truncatus	ENSTTRG00000011524	3 retrocopies	retro_ttru_268, retro_ttru_510, retro_ttru_588,