RetrogeneDB ID: retro_mdom_1897

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:17913785..17914297(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSMODG00000007323
• Aliases: None
• Description: RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]

Sequence

>retro_mdom_1897
GGGAGGGTTGGAAAATCTGCCCTGACTGTACAGTTTGTTCAAAGAATATTTGTTGAAAACTATGATCCCACGATAGAAGA
TTCTTATAGAAAGCAAGTTGAAGTAGATGCTCAACAATGCGTGCTTGAAATCTTGGACACTGCAGGGAAGGAACAATTTA
TGGCATGAGAGATTTGTACGAAAAATGGGCAAGGCTTTGCATTAGTCTACTCTATCACAGCACAATCCACATTTAATGAT
CTACAAGATCTTTGAGAACAAATACTTCGAGTTAAAGACGCCAATGATGTGCCAATGTTCTTGTTGACAATAAGTGTGAC
TTGGAAGATGAAAGAGTTGTAGGAAAAGAGCAAGGACAGAACCTAGCAAGACAATGGAACAACTGTGAGTTCTTGGAATC
CTCTGCTAAATCAAAGGTAAACGTTAATGAGATCTTTTATGATCTAGTCCGGCTAATTAACAGAAAAACTCCAGTGCCTG
GGAAGGCACCTAAAAATACATCATGTCAATTG

Alignment

ORF - retro_mdom_1897 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.13 %
• Parental protein coverage: 93.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALV
          G.VGKSALTVQFVQ.IFVE.YDPTIEDSYRKQVEVDAQQC.LEILDTAG.EQF.A......KNGQGFALV
Retrocopy GRVGKSALTVQFVQRIFVENYDPTIEDSYRKQVEVDAQQCVLEILDTAGKEQFMA*-EICTKNGQGFALV

Parental  YSITAQSTFNDLQDLREQILRVKDTDDVPM-ILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKS
          YSITAQSTFNDLQDL.EQILRVKD..DVPM..LV.NKCDLEDERVVGKEQGQNLARQWNNC.FLESSAKS
Retrocopy YSITAQSTFNDLQDL*EQILRVKDANDVPM<VLVDNKCDLEDERVVGKEQGQNLARQWNNCEFLESSAKS

Parental  KINVNEIFYDLVRQINRKTPVPGKARKKSSCQL
          K.NVNEIFYDLVR.INRKTPVPGKA.K..SCQL
Retrocopy KVNVNEIFYDLVRLINRKTPVPGKAPKNTSCQL

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_1897 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1897 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
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dipodomys ordii	ENSDORG00000001086	1 retrocopy	retro_dord_521,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Homo sapiens	ENSG00000127314	2 retrocopies	retro_hsap_3338, retro_hsap_4234,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Myotis lucifugus	ENSMLUG00000016606	2 retrocopies	retro_mluc_1126, retro_mluc_2211,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327, retro_mdom_139, retro_mdom_1777,
Monodelphis domestica	ENSMODG00000004590	1 retrocopy	retro_mdom_51,
Monodelphis domestica	ENSMODG00000007323	5 retrocopies	retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897 , retro_mdom_429,
Monodelphis domestica	ENSMODG00000017458	1 retrocopy	retro_mdom_153,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Procavia capensis	ENSPCAG00000010977	1 retrocopy	retro_pcap_8,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tursiops truncatus	ENSTTRG00000015712	2 retrocopies	retro_ttru_1105, retro_ttru_134,
Vicugna pacos	ENSVPAG00000000931	2 retrocopies	retro_vpac_283, retro_vpac_408,