RetrogeneDB ID: retro_itri_1677

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393629.1:264677..265260(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB1B
• Ensembl ID: ENSSTOG00000011052
• Aliases: None
• Description: RAB1B, member RAS oncogene family [Source:HGNC Symbol;Acc:18370]

Sequence

>retro_itri_1677
GATTATTTATTCAAGTTACTTCTGATTGGCGATTCTGGGGTTGGAAAGACTTGCCTTCTTCTTAGGTTTGCAAATGACAC
ATATACAGAAAGCTACATCAGCACAATTGGTGTGGATTTCAAAATAAGAACTATAGAGTCAGATGGGAAAACAATTAAGC
TTCGAATATAGGACACAGCAGGCCAAGAAAGATTTCAAAAAATCACCTCCAGTTACTACAGAGGAACCCATGGCATTATA
GTTGTGTATGATGTGACAGATCAGGAGTCCTTCAATAATGTTAAATAGTGGCTGCATGAAATAGATCGTTATGCTAGTGA
AAATGTCAACAAGTTGTTGGTAGGAAACAAATGTGATCTGACCACAAAGAAAGTAGTGGACTACAACAGCAAAGGAATTT
GCTGATTCCCTTGGAATCTCATTTTTGGAAACTAAGAACGCAACGAATGTAGAATAGTCTTTCATGATGATGGCAGCTGA
GATTAAAAAGCCAATGGGCCCTGGAGCAAAAGCTGGTGGCACAGAGAAGTCCAACGTTAAAATTCAGAGCACTCCAGTCA
AGCAGTCAGGTGGAGGTTGCTGC

Alignment

ORF - retro_itri_1677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITS
          DYLFKLLLIGDSGVGK.CLLLRFA.DTYTESYISTIGVDFKIRTIE.DGKTIKL.I.DTAGQERF..ITS
Retrocopy DYLFKLLLIGDSGVGKTCLLLRFANDTYTESYISTIGVDFKIRTIESDGKTIKLRI*DTAGQERFQKITS

Parental  SYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDN-TTAKEFADSLG
          SYYRG.HGIIVVYDVTDQES..NVK.WL.EIDRYASENVNKLLVGNK.DL.T.K.V...TTAKEFADSLG
Retrocopy SYYRGTHGIIVVYDVTDQESFNNVK*WLHEIDRYASENVNKLLVGNKCDL-TTKKVVD>TTAKEFADSLG

Parental  IPFLETSAKNATNVEQAFMTMAAEIKKRMGPGAASGG-ERPNLKIDSTPVKPAGGGCC
          I.FLET..KNATNVE..FM.MAAEIKK.MGPGA..GG.E..N.KI.STPVK..GGGCC
Retrocopy ISFLET--KNATNVE*SFMMMAAEIKKPMGPGAKAGGTEKSNVKIQSTPVKQSGGGCC

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1677 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1677 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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,
Ictidomys tridecemlineatus	ENSSTOG00000011052	1 retrocopy	retro_itri_1677 ,
Ictidomys tridecemlineatus	ENSSTOG00000020693	1 retrocopy	retro_itri_1541,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,