RetrogeneDB ID: retro_itri_1394

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393472.1:1397600..1398023(-)
• Located in intron of: ENSSTOG00000016095

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015375
• Aliases: None
• Description: None

Sequence

>retro_itri_1394
TACATTAAAACAAACAAATGCCCTTTGCCATCACTTGGTCTCTGAGGTCTCAGAGCCACCCTTCCTGCTTCCATGAGTTC
TAAGGGAAAGATCATAGAATTCCAGAGTGATGATTCTGATGAATGCCACAACCATGGAAGTCAGGATTAATCACCTGAGA
GTGCTTCTGGCATACGACAGAGAAAATGCCAGGAGATGCCCCAGAAGCCAGCAAGGGAAGAACAGGATCTGAAGGGAGGG
CCAGAAGCAGCTGGCTCCAAACAGTCTCAGAGACAAGTGCACCCACTGGGAAAGGAAGGACTTCTGGGAAGCAAAGAGAG
GGCGTCAGGACCCAGGAAAGACAGTGGGAGTATCTGGAGCCACAGAGCCTGGGAAAGGAAGTACCTCAGGGCATATGAAG
AGATCAGCGACTCTGAGGAGAAG

Alignment

ORF - retro_itri_1394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 73.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YLKRNYTTMTSL---GLRATLPAFMSSNRQIIESQSDDSDECRNRGSQDELPKSASGIRQRKRKEKMPKK
          Y.K.N.....SL...GLRATLPA.MSS...IIE.QSDDSDEC.N.GSQD..P.SASGIRQRK..E.MP.K
Retrocopy YIKTNKCPLPSLGL*GLRATLPASMSSKGKIIEFQSDDSDECHNHGSQD*SPESASGIRQRKCQE-MPQK

Parental  PAMEENDPKGVPKAVGSEQAQRQLYPLGKASTSGKQSEKVSGPRKKNVNIWSHRLRERKYLVAYEEISDP
          PA.EE.D.KG.P.A.GS.Q.QRQ..PLGK....G...E..SGPRK....IWSHR..ERKYL.AYEEISD.
Retrocopy PAREEQDLKGGPEAAGSKQSQRQVHPLGKEGLLGSK-ERASGPRKDSGSIWSHRAWERKYLRAYEEISDS

Parental  EEE
          EE.
Retrocopy EEK

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_1394 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1394 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014776	1 retrocopy	retro_cjac_2373,
Homo sapiens	ENSG00000204645	1 retrocopy	retro_hsap_3512,
Gorilla gorilla	ENSGGOG00000026107	1 retrocopy	retro_ggor_2374,
Macaca mulatta	ENSMMUG00000019164	1 retrocopy	retro_mmul_1862,
Nomascus leucogenys	ENSNLEG00000003504	1 retrocopy	retro_nleu_482,
Pongo abelii	ENSPPYG00000020365	1 retrocopy	retro_pabe_2903,
Pan troglodytes	ENSPTRG00000021857	1 retrocopy	retro_ptro_2385,
Ictidomys tridecemlineatus	ENSSTOG00000015375	3 retrocopies	retro_itri_1394 , retro_itri_1855, retro_itri_746,