RetrogeneDB ID: retro_itri_1541

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393535.1:578346..578864(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB1A
• Ensembl ID: ENSSTOG00000020693
• Aliases: None
• Description: RAB1A, member RAS oncogene family [Source:HGNC Symbol;Acc:9758]

Sequence

>retro_itri_1541
ATGTCCAGCATGAATCCCAAATATGATTATTAATTCAAGTTACTTCTGATTGGTGACTCTGGGGTTGGAAAGTCTTGTCT
CCTTTTTAGGTTTGCAGATGATACATATACAGAAAGCTACATCAGCACAATTGGTGAGGATTTCAAAATAAGAACTATAG
ATGGGAAAACAATCAAGCTTCAAATATGGGACACAGCAGGCCAAGAAAGATGCCCAACAATCACCTCCAGTTATTACAGA
GGAGCCCATGGCATCATGGTTGTGTATGATGTGACAGATCAGGAGTCCTTCAATAATGTTAAACAGTGGCTGCAGGAAAT
AGATCCTTATGCCAGTGAAAATGTCAACAAGTTGTTGGTAGGGAATCCATATGATCTGACCCAAAGAAACTAGTAGACTA
CACAAAAGCAAAGGAATTTGCTAATTTCTTTGGAATTCCATTTTTAGAAACCAGTGCTAAGAACACAACAAATGTATCAC
TGTCTTTTATGATGATAGCAGCTGAGATTAAAAGCAGG

Alignment

ORF - retro_itri_1541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.8 %
• Parental protein coverage: 85.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSMNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQ
          MSSMNP.YDY.FKLLLIGDSGVGKSCLL.RFADDTYTESYISTIG.DFKIRTI..DGKTIKLQIWDTAGQ
Retrocopy MSSMNPKYDY*FKLLLIGDSGVGKSCLLFRFADDTYTESYISTIGEDFKIRTI--DGKTIKLQIWDTAGQ

Parental  ERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLT-TKKVVDYTTA
          ER..TITSSYYRGAHGI.VVYDVTDQESFNNVKQWLQEID.YASENVNKLLVGN..DLT..KK.VDYT.A
Retrocopy ERCPTITSSYYRGAHGIMVVYDVTDQESFNNVKQWLQEIDPYASENVNKLLVGNPYDLT<PKKLVDYTKA

Parental  KEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKR
          KEFA...GIPFLETSAKN.TNV..SFM..AAEIK.R
Retrocopy KEFANFFGIPFLETSAKNTTNVSLSFMMIAAEIKSR

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_1541 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1541 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002205	2 retrocopies	retro_etel_1687, retro_etel_413,
Homo sapiens	ENSG00000138069	2 retrocopies	retro_hsap_2362, retro_hsap_3626,
Macaca mulatta	ENSMMUG00000021721	1 retrocopy	retro_mmul_951,
Oryctolagus cuniculus	ENSOCUG00000017003	1 retrocopy	retro_ocun_800,
Pongo abelii	ENSPPYG00000012360	1 retrocopy	retro_pabe_2135,
Pan troglodytes	ENSPTRG00000011989	1 retrocopy	retro_ptro_1727,
Rattus norvegicus	ENSRNOG00000004992	1 retrocopy	retro_rnor_110,
Ictidomys tridecemlineatus	ENSSTOG00000011052	1 retrocopy	retro_itri_1677,
Ictidomys tridecemlineatus	ENSSTOG00000020693	1 retrocopy	retro_itri_1541 ,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,