RetrogeneDB ID: retro_itri_1550

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393537.1:791537..792142(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000020756
• Aliases: None
• Description: None

Sequence

>retro_itri_1550
GAAAAGGAAGACAAGGACAAAAACAAAGAACAGATCCCAAGGAAGATACTCTCTAGAGACTCCAGCCAAGAATATACAGA
CTCCTCTGGAATAGACCTACATGAATTTCTTGTAAATACACTGAAAAAAAACCCAAGGGACAGAATGATGCTGCTAAAAT
TAGAATGGGAGATTCTGGAATTTATTAATGACAACAATAACCAGTTCAAGAAGTTCCCTCAGATGACCTCATATCACCAG
ATGCTATTACACTGGGTAGCTGCCTATTTTGGAATGGACCACAATGTTGATCAAACTGGGAAAGCTGTAATCATCAACAA
AACCAGGAACACAAGAGTCCCTGAACAGAGTTTCTCAGAACATATAAAGGATAGGAAGAATACTGAATTTCAACAGAGAT
TAATCCTCAAGAGAGATGATGCCAGTATGGACCGAGATGATAACCAGATCAGAGTTCCATTGCAGGATGGAAGGAGGAGC
AAGTCAATAGAAAAGAGAGAGGAGAAATATCAAAGGGTCTGAGAGAGAATATTTGCCTGAGAGACTGGCCAGAACGGATA
TCTAAATGACATCGGGGGAACCGAGAAGGGCTGAGTCGTACTTCA

Alignment

ORF - retro_itri_1550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 61.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKEDKDKNKEKVPRKMLSRDSSQEYTDSTGIDLHEFLVNTLKKNPRDRMMLLKLEQEILEFINDNNNQFK
          EKEDKDKNKE..PRK.LSRDSSQEYTDS.GIDLHEFLVNTL...PRDRMMLLKLE.EILEFINDNNNQFK
Retrocopy EKEDKDKNKEQIPRKILSRDSSQEYTDSSGIDLHEFLVNTLXXXPRDRMMLLKLEWEILEFINDNNNQFK

Parental  KFPQMTSYHRMLLHRVAAYFGMDHNVDQTGKAVIINKTSNTRIPEQRFSEHIKDEKNAEFQQRFILKRDD
          KFPQMTSYH.MLLH.VAAYFGMDHNVDQTGKAVIINKT.NTR.PEQ.FSEHIKD.KN.EFQQR.ILKRDD
Retrocopy KFPQMTSYHQMLLHWVAAYFGMDHNVDQTGKAVIINKTRNTRVPEQSFSEHIKDRKNTEFQQRLILKRDD

Parental  ASMDRDDNQIRVPLQDGRRSKSIEEREEEYQRVRERIFARETGQNGYLNDI-RLSKEAFSSSS
          ASMDRDDNQIRVPLQDGRRSKSIE.REE.YQRV.ERIFA.ETGQNGYLNDI.R...E..S..S
Retrocopy ASMDRDDNQIRVPLQDGRRSKSIEKREEKYQRV*ERIFA*ETGQNGYLNDI<RGNREGLSRTS

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_1550 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1550 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018361	1 retrocopy	retro_btau_637,
Macaca mulatta	ENSMMUG00000021789	1 retrocopy	retro_mmul_1848,
Ictidomys tridecemlineatus	ENSSTOG00000020756	1 retrocopy	retro_itri_1550 ,