RetrogeneDB ID: retro_itri_14

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393426.1:1880166..1880700(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000014673
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: COPZ2
• Ensembl ID: ENSSTOG00000027550
• Aliases: None
• Description: coatomer protein complex, subunit zeta 2 [Source:HGNC Symbol;Acc:19356]

Sequence

>retro_itri_14
ATGGAGGTGCTGATTTTGGAACCCTCCCTGTATACTGTCAAAGCCATCCTGATTCTGGACAATGATGGAGACCGACTTTT
TGCCAAGTACTATGACGACACCTACCCCAGTGTCAAGGAGCAAAAGGCCTTTGAAAAGAATATTTTCAACAAGACCCATC
GGACTGACAGTGAAATTGCCCTCTTGGAAGGCCTGACGGTGGTGTATAAAAGCAGCATCGATCTCTATTTCTGTGTGATT
GGCAGCTCCTATGAAAATGAGTTGATGCTTATGGCTGTTCTGAATTGCCTCTTTGACTCCTTGAGCCAGATGCTGAGGAA
AAATGTAGAAAAACGAGCTCTGCTGGAGAACGTGGAGGGGCTCTTCTTGGCTGTGGATGAAATCGTAGATGGAGGGGTGA
TACTAGAGAGGGATCCCCAGCAAGTTGTACACCGGGGGGCATTGAGGGGTGAAGATGTACCCTTAACGGAGCAGACCGTG
TCTCAGGTGCTTCAGTCAGCTAAAGAACAGATCAAGTGGTCACTCCTCCCGTGA

Alignment

ORF - retro_itri_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.94 %
• Parental protein coverage: 97.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPSLYTIKAVFILDNDGRRLLAKYYDDTFPSMKEQMVFEKNVFNKTSRTESEIAFFGGMTIVYKSSIDLF
          EPSLYT.KA..ILDNDG.RL.AKYYDDT.PS.KEQ..FEKN.FNKT.RT.SEIA...G.T.VYKSSIDL.
Retrocopy EPSLYTVKAILILDNDGDRLFAKYYDDTYPSVKEQKAFEKNIFNKTHRTDSEIALLEGLTVVYKSSIDLY

Parental  LYVVGSSHENELMLMSVLTCLFESLSHILRKNVEKRWLLENMDGAFLVLDEIVDGGVILESDPQQVIQKV
          ..V.GSS.ENELMLM.VL.CLF.SLS..LRKNVEKR.LLEN..G.FL..DEIVDGGVILE.DPQQV....
Retrocopy FCVIGSSYENELMLMAVLNCLFDSLSQMLRKNVEKRALLENVEGLFLAVDEIVDGGVILERDPQQVVHRG

Parental  NFRADDSSLTEQSVTQVLQSAKEQIKWSLL
          ..R..D..LTEQ.V.QVLQSAKEQIKWSLL
Retrocopy ALRGEDVPLTEQTVSQVLQSAKEQIKWSLL

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_14 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_14 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000027550	1 retrocopy	retro_itri_14 ,