RetrogeneDB ID: retro_mdom_1975

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:32494355..32495110(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZRANB2
• Ensembl ID: ENSMODG00000000504
• Aliases: None
• Description: zinc finger, RAN-binding domain containing 2 [Source:HGNC Symbol;Acc:13058]

Sequence

>retro_mdom_1975
ATGATGAAAGCTGGTGGGACTGAAATAGGAAAGACGCTCGCTGAGAAGAGCTGAGGTCTATTTAGTGCTAACGACTGGCA
GTGTAAAACTAATGTGAATTGGGCCAGGAGATCTGAATATAATGTGCAATACTCCCAAGTATGCTAAAACTAGAGGAAAG
GACTGGATACCGTGGAGGTTTTAATGAAAGAGAAAATGTGGAGTATATTGAATGAGAGGAGTCTGACAGAGAATATGATG
AGTTTGGTCAGAAAAAGAAAAAGTATAGAGGGAAAGCAGTAGTACCTGCCTCTATCTTAAAGGAAATTGAGGATAAAGAG
TCCAAGGGAGAAGAAGAGGATGAGGATGAAGATCTATCCAAATACAAATTGAATGAGGATGAGGATGAAGATGATGCAGA
CCTATCAAAATATAATCTTGATGCCAGTGAAGAGGAAGATGGCAATAAAAAGAAATCCCACTGAAGAAGTCACTCCAAGT
CTCAATCTTCCCACTCCTGATCTTCATCTCGCTCATCCTCCCACTCAAGCTCAAGATCTAGGTCCAGGTCCCACTCAGGA
AGCTCCTCCAGCTCCTGGTAAAGGTCTCGGTCCAGTTCCAGAGAACTCTTGAGATCTCGTGGGTCGAAATCCAGATCCAG
CTCCAGGTCCCACAGAGGGTCTTCCTCCCCATGAAAAAGATCTTATTCAAGTTCCTTATCATCTCCCAAGAGAGGCAGCA
AACGAAGCCATTCTAGATCTTCTTCACTTGGTGAT

Alignment

ORF - retro_mdom_1975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.06 %
• Parental protein coverage: 88.5 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMKAGGTEIGKTLAEKSRGLFSANDWQCKTCSNVNWARRSECNM-CNTPKYAKLEERTGYGGGFNERENV
          MMKAGGTEIGKTLAEKS.GLFSANDWQCKT..NVNWARRSE.N.....P...KLEERTGY.GGFNERENV
Retrocopy MMKAGGTEIGKTLAEKS*GLFSANDWQCKT--NVNWARRSEYNV<AILPSMLKLEERTGYRGGFNERENV

Parental  EYIEREESDGEYDEFGRKKKKYRGKAVGPASILKEVEDKESEGEEEDEDEDLSKYKLDEDEDEDDADLSK
          EYIE.EESD.EYDEFG.KKKKYRGKAV.PASILKE.EDKES.GEEEDEDEDLSKYKL.EDEDEDDADLSK
Retrocopy EYIE*EESDREYDEFGQKKKKYRGKAVVPASILKEIEDKESKGEEEDEDEDLSKYKLNEDEDEDDADLSK

Parental  YNLDASEEEDGNKKKSHRRSRSKSRSSHSRSSSRSSSHSSSRSRSRSRSGSSSSSRSRSRSSSRELSRSR
          YNLDASEEEDGNKKKSH.RS.SKS.SSHS.SSSRSSSHSSSRSRSRS.SGSSSSS..RSRSSSREL.RSR
Retrocopy YNLDASEEEDGNKKKSH*RSHSKSQSSHS*SSSRSSSHSSSRSRSRSHSGSSSSSW*RSRSSSRELLRSR

Parental  GSKSRSSSRSHRGSSSPRKRSYSSSSSSPERGSKRSRSRSSSPGD
          GSKSRSSSRSHRGSSSP.KRSYSSS.SSP.RGSKRS.SRSSS.GD
Retrocopy GSKSRSSSRSHRGSSSP*KRSYSSSLSSPKRGSKRSHSRSSSLGD

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_1975 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1975 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006356	2 retrocopies	retro_cjac_2350, retro_cjac_4199,
Macaca mulatta	ENSMMUG00000017312	2 retrocopies	retro_mmul_2602, retro_mmul_2618,
Monodelphis domestica	ENSMODG00000000504	2 retrocopies	retro_mdom_1975 , retro_mdom_443,
Oryctolagus cuniculus	ENSOCUG00000004640	2 retrocopies	retro_ocun_1170, retro_ocun_776,
Otolemur garnettii	ENSOGAG00000000485	4 retrocopies	retro_ogar_1274, retro_ogar_1841, retro_ogar_2843, retro_ogar_976,
Pan troglodytes	ENSPTRG00000000856	1 retrocopy	retro_ptro_3251,
Tupaia belangeri	ENSTBEG00000002316	3 retrocopies	retro_tbel_122, retro_tbel_3653, retro_tbel_4007,