RetrogeneDB ID: retro_shar_68

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867627.1:70845..71460(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000003677
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAB1B
• Ensembl ID: ENSSHAG00000010376
• Aliases: None
• Description: RAB1B, member RAS oncogene family [Source:HGNC Symbol;Acc:18370]

Sequence

>retro_shar_68
GCTGCCACCATGAATGCCGAGTGTGATTACCTGTTTAAACTGTTGCTGATCGGGGATTCGGGTGTGGGCAAATCTTGTCT
ACTGCTGCGCTTCGCCGACAACAAGTACAGCGATGATTACGCCTGTACCATTGGCGTGGATTTCAAGATCCGTACTATCC
AACTGAATGGTAAAATTGTGAAGCTGCAGATCTGGGACACCGCTGGCCAGGAACGCTTTCACACCATCACCTCAAGCTAT
TATCGGGGAGCCCATGGCGTTATCCTGGTGTATGATGTGAGCAGCCTTGAGTCCTTTGTCAACGTGAAGCAGTGGCTGGT
CGAAGTGGAGCTCCGTGGCAGCGAAACCACCGACAAGGTATTGGTGGGCAATAAGAGCGACCTTGTTACCGAGAGAATGG
TAGACTCTCTCATGGCCAAGGAGTTCGCCGATTCCCTGGGCATCCCTTTCCTGGAGACCAGTGCCAAGAACGCCATTAAT
GTCGAGCAAGTCTTCCTCACCATCGCGGCCGAGATCAGGGAGCACCTCAGATGTGAGCCGTTTTCTGCCAGGGATCTCCC
TGCACTCAAGGTTAACAGCTCTCCTGTGAAGATGGCGTGTGGGGGTTGCTGTTAA

Alignment

ORF - retro_shar_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.5 %
• Parental protein coverage: 99.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSSSDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFR
          ....DYLFKLLLIGDSGVGKSCLLLRFAD..Y...Y..TIGVDFKIRTI.L.GK..KLQIWDTAGQERF.
Retrocopy NAECDYLFKLLLIGDSGVGKSCLLLRFADNKYSDDYACTIGVDFKIRTIQLNGKIVKLQIWDTAGQERFH

Parental  TITSSYYRGAHGIIVVYDVTDQESYANVKQWLEEINRYASENVNKLLVGNKSDLTTKKVVDNPTAKEFAD
          TITSSYYRGAHG.I.VYDV...ES..NVKQWL.E.....SE...K.LVGNKSDL.T...VD...AKEFAD
Retrocopy TITSSYYRGAHGVILVYDVSSLESFVNVKQWLVEVELRGSETTDKVLVGNKSDLVTERMVDSLMAKEFAD

Parental  SLGIPFLETSAKNATNVEQAFMTMAAEIKKRMGPGAASGGERPNLKIDSTPVKPASGGCC
          SLGIPFLETSAKNA.NVEQ.F.T.AAEI.........S....P.LK..S.PVK.A.GGCC
Retrocopy SLGIPFLETSAKNAINVEQVFLTIAAEIREHLRCEPFSARDLPALKVNSSPVKMACGGCC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_68 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 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,
Pongo abelii	ENSPPYG00000003031	1 retrocopy	retro_pabe_3386,
Pan troglodytes	ENSPTRG00000003915	1 retrocopy	retro_ptro_2892,
Sarcophilus harrisii	ENSSHAG00000010376	1 retrocopy	retro_shar_68 ,
Sarcophilus harrisii	ENSSHAG00000018522	1 retrocopy	retro_shar_676,
Ictidomys tridecemlineatus	ENSSTOG00000011052	1 retrocopy	retro_itri_1677,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,