RetrogeneDB ID: retro_mdom_196

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:23989575..23990181(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000022797
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAB1B
• Ensembl ID: ENSMODG00000008371
• Aliases: None
• Description: RAB1B, member RAS oncogene family [Source:HGNC Symbol;Acc:18370]

Sequence

>retro_mdom_196
ATGAGTGGAGATTATGATTACTTGTTTAAGGTGCTGCTGATTGGAGATTCAGGTGTGGGCAAATCCTGCCTGCTACTTCG
CTTTGCGGATGACACCTACAGTGACAGCTATGTTAGTACCATTGGTGTGGACTTTAAGATCAGAACAATCCAATTAGATG
GCAAGATTGTGAAACTGCAGATTTGGGATACTGCGGGACAGGAGAGATTCCGTACCATTACCTCGAGCTACTACCATGGG
GCCCATGGTATTATCTTGGTGTATGATGTGAGTGATCCCAAGTCCTATGCCAACGTGAAGCAATGGCTGATTGAGGTGGA
GCGCCATGCGAACAGAAACACTAACAAGCTGCTAGTGGGCAACAAGAGTGACCTTGTTACCAAGAATATGGTGGACCGCA
CCATAGCCAAAGAGTTCGCTGACTCCATAGGCATCCCCTTTCTAGAAACCAGCGCCAAAAACTCCATTAATGTGGATGAA
GTCTTCCTCACCATGGCCTCTGTGATCAAGAAACGCATTAAAGCTTTACCCGTTTCCACCAGCGACTTCCCCATCATCAC
GTTCAACAGCTCTCCTGTGAAGTCTGCGTCTGGGAGTTGTTGCTAA

Alignment

ORF - retro_mdom_196 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERF
          M...YDYLFK.LLIGDSGVGKSCLLLRFADDTY..SY.STIGVDFKIRTI.LDGK..KLQIWDTAGQERF
Retrocopy MSGDYDYLFKVLLIGDSGVGKSCLLLRFADDTYSDSYVSTIGVDFKIRTIQLDGKIVKLQIWDTAGQERF

Parental  RTITSSYYRGAHGIIVVYDVTDQESYANVKQWLEEINRYASENVNKLLVGNKSDLTTKKVVDNPTAKEFA
          RTITSSYY.GAHGII.VYDV.D..SYANVKQWL.E..R.A..N.NKLLVGNKSDL.TK..VD...AKEFA
Retrocopy RTITSSYYHGAHGIILVYDVSDPKSYANVKQWLIEVERHANRNTNKLLVGNKSDLVTKNMVDRTIAKEFA

Parental  DSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMGPGAASGGERPNLKIDSSPVKPASGGCC
          DS.GIPFLETSAKN..NV...F.TMA..IKKR......S....P.....SSPVK.ASG.CC
Retrocopy DSIGIPFLETSAKNSINVDEVFLTMASVIKKRIKALPVSTSDFPIITFNSSPVKSASGSCC

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_196 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_196 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001599	1 retrocopy	retro_cjac_931,
Homo sapiens	ENSG00000174903	1 retrocopy	retro_hsap_4252,
Gorilla gorilla	ENSGGOG00000009755	2 retrocopies	retro_ggor_1792, retro_ggor_2850,
Macropus eugenii	ENSMEUG00000000023	1 retrocopy	retro_meug_1985,
Monodelphis domestica	ENSMODG00000008371	1 retrocopy	retro_mdom_196 ,
Monodelphis domestica	ENSMODG00000015821	1 retrocopy	retro_mdom_1577,
Pongo abelii	ENSPPYG00000003031	1 retrocopy	retro_pabe_3386,
Pan troglodytes	ENSPTRG00000003915	1 retrocopy	retro_ptro_2892,
Sarcophilus harrisii	ENSSHAG00000010376	1 retrocopy	retro_shar_68,
Ictidomys tridecemlineatus	ENSSTOG00000011052	1 retrocopy	retro_itri_1677,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,