RetrogeneDB ID: retro_itri_1540

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393533.1:1563595..1563874(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPV
• Ensembl ID: ENSSTOG00000012221
• Aliases: None
• Description: centromere protein V [Source:HGNC Symbol;Acc:29920]

Sequence

>retro_itri_1540
TTCATTGTTCCAGAGTCTTACTTCAAGCTCCCAAAGGGGCATAAAAGGATGACAACCTATATGTTTATATGTTCAACAAA
CACTAAGCGCAACACACCTTCTCTAAGAGTGGTGGCTTTCAGAGCTTCTGAACTCCCACTCAATACCAGGGAGGTTTCAG
ATTGTCCTAGGCCATCTAGATAAGGACACTTTGAAGTGTCAGGTCATAGAGTAATTCATTGGCAGCAATTGGGAGAAGGC
CATAAAACAGCATAGGTCATCAGCAATATGTCTAAAGAT

Alignment

ORF - retro_itri_1540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.61 %
• Parental protein coverage: 52.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FIVPASRFKLL-KGA---ESITTYTFNTHKAQHTFCKKCGVQSFYTP-RSNPGGFGIAPHCLDEGTVRSV
          FIVP.S.FKL..KGA........Y.FN.H.AQHTF.K..G.QSF.TP..S.PG.F.I....LD..T....
Retrocopy FIVPESYFKLP<KGA*KDDNLYVYMFNKH*AQHTFSKSGGFQSF*TP<HSIPGRFQIVLGHLDKDTLKCQ

Parental  VTEEFNGSNWEKAMKEHKT-IKNMSKE
          V.E.F.GSNWEKA.K.H...I.NMSK.
Retrocopy VIE*FIGSNWEKAIKQHRS<ISNMSKD

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_1540 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1540 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004716	5 retrocopies	retro_amel_1859, retro_amel_1870, retro_amel_1909, retro_amel_1926, retro_amel_924,
Canis familiaris	ENSCAFG00000018019	2 retrocopies	retro_cfam_2153, retro_cfam_2155,
Homo sapiens	ENSG00000166582	3 retrocopies	retro_hsap_4683, retro_hsap_4833, retro_hsap_4834,
Macropus eugenii	ENSMEUG00000002027	1 retrocopy	retro_meug_519,
Microcebus murinus	ENSMICG00000007166	1 retrocopy	retro_mmur_1491,
Mustela putorius furo	ENSMPUG00000010146	2 retrocopies	retro_mputfur_1195, retro_mputfur_39,
Nomascus leucogenys	ENSNLEG00000014726	1 retrocopy	retro_nleu_2709,
Otolemur garnettii	ENSOGAG00000029365	1 retrocopy	retro_ogar_99,
Pan troglodytes	ENSPTRG00000008810	1 retrocopy	retro_ptro_3216,
Ictidomys tridecemlineatus	ENSSTOG00000012221	2 retrocopies	retro_itri_110, retro_itri_1540 ,