RetrogeneDB ID: retro_itri_781

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393321.1:8016951..8017278(-)
• Located in intron of: ENSSTOG00000000315

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRB3
• Ensembl ID: ENSSTOG00000002396
• Aliases: None
• Description: crumbs homolog 3 (Drosophila) [Source:HGNC Symbol;Acc:20237]

Sequence

>retro_itri_781
GCCCTGGAGCTGCTCTTGCTGCCGGCCCTCTTGGGCCGAGCCTGGGGGCACGCTACCACAGCACTGAACCCTTCGGAGAC
TGGCACTATCACGCCCTCTGTCCCCAGCCCCAGTGAGGGTCTGTCTCAGGAGGCCATTACTTCTGTCATCGTGGTTTTCT
CCCTCCTGGCCACCTTGCTCCTGGCCGTGGGGCTGGCGCTACTGGTACAGAAACTTTGGGAGAAGCGGCAGACAGAGGGC
ACCTACCGGCCCAGCAGCGAGGAGCAGGTGGGTGCCTGCGCGCCACCGCCCCCCAATCTCAAGTTGCCTCCGGAGGAGCG
GCTCATC

Alignment

ORF - retro_itri_781 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 91.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALGLPLLPALLGRAWGQATTALNTSSGNGTTPPSTPSP-RGLSPEAITAIIVVFSILAALLLAMGLVLLV
          AL.L.LLPALLGRAWG.ATTALN.S...GT..PS.PSP..GLS.EAIT..IVVFS.LA.LLLA.GL.LLV
Retrocopy ALELLLLPALLGRAWGHATTALNPSE-TGTITPSVPSPSEGLSQEAITSVIVVFSLLATLLLAVGLALLV

Parental  RKLREKRQTEGTYRPSSEEQVGARAPPPPNLKLPPEERLI
          .KL.EKRQTEGTYRPSSEEQVGA.APPPPNLKLPPEERLI
Retrocopy QKLWEKRQTEGTYRPSSEEQVGACAPPPPNLKLPPEERLI

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_781 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_781 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016567	1 retrocopy	retro_cjac_868,
Homo sapiens	ENSG00000130545	2 retrocopies	retro_hsap_2747, retro_hsap_3478,
Gorilla gorilla	ENSGGOG00000007070	2 retrocopies	retro_ggor_1910, retro_ggor_2345,
Macaca mulatta	ENSMMUG00000005599	1 retrocopy	retro_mmul_1434,
Nomascus leucogenys	ENSNLEG00000015936	1 retrocopy	retro_nleu_1543,
Pongo abelii	ENSPPYG00000009457	2 retrocopies	retro_pabe_2222, retro_pabe_2873,
Pan troglodytes	ENSPTRG00000010367	1 retrocopy	retro_ptro_2984,
Rattus norvegicus	ENSRNOG00000047322	1 retrocopy	retro_rnor_1506,
Ictidomys tridecemlineatus	ENSSTOG00000002396	1 retrocopy	retro_itri_781 ,