RetrogeneDB ID: retro_itri_706

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393313.1:9902143..9903002(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000024757
• Aliases: None
• Description: None

Sequence

>retro_itri_706
GTTGAGGGCCTCTCCCGGCAGGTGAAGCATGTTATGAACTTTACTAACTGGGCAACTGCTAGTGGCAACAGCACAGCACT
ACTGTACAGCAAGCGACTGATTACTTTTCAATTGCATCATATTTTGAAAGCACGATGTGATCCTGTTCCTGCTGCTAATG
GATCAATACGTTTCCATTGTGATCCTACCTTCTGGGCAAAGAATGTAGTCAATTTAGGTAATCTAGTAATAGAGAGTAAA
CCAGCTCCTGGTTATACTCCTAATGTTGTAGTTGGGCAAGTTCCTACAGGGACAAACCACATTAGTAAAACCCCTGGACA
GATTAATTTAAGCACAGCTTCTACTCCAACACATGCAACAACAAGTATATGCTCAGAAACATCAGCAGTTGCAACAGATG
AGGATGCAGCAACCACCAGCTCCTGTACCAACAACAACAACAACTCAACAGCATCTTAAACAAGCAGCTCCTCAGATGTT
ACAACAACAGCCTCCAAGATTAATCAGTGTGCAAACCATGCAAAGAGGCAACATGAACTGTGGAGCTTTTCAAGCCCATC
AAATGAGACTGGCTCAGAATGCTGCCAGAATACCAGGGATACCCAGGCACAGTGGCCCTCAATATTCCATGATGCAGCCA
CATCTCCAAAGACAACACTCAAACCCAGGGCATGCTGGACCCTTTCCTGTTGTATCGGTACACAACACCAAAATCAACCC
AACAAGCCCTACTACAGCAACTATGGCCAATGCAAACTGAGGTCCCACCAGCCCATCTGTTACAGCAATAGAGCTTATCC
CCTCAGTTACCAATCCAGAAAACCTTCCATCATTGCCAGATATTCCACCCATACAGTTG

Alignment

ORF - retro_itri_706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.79 %
• Parental protein coverage: 75.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ITGLSRQVKHVMNFTNWAIASGSSTALLYSKRLITFQLRHILKARCDPVPAANGAIRFHCDPTFWAKNVV
          ..GLSRQVKHVMNFTNWA.ASG.STALLYSKRLITFQL.HILKARCDPVPAANG.IRFHCDPTFWAKNVV
Retrocopy VEGLSRQVKHVMNFTNWATASGNSTALLYSKRLITFQLHHILKARCDPVPAANGSIRFHCDPTFWAKNVV

Parental  NLGNLVIESKPAPGYTPNVVVGQVPPGTNHISKTPGQINL-AQLRLQHMQQQVYAQKHQQLQQMRMQQPP
          NLGNLVIESKPAPGYTPNVVVGQVP.GTNHISKTPGQINL.AQL.LQHMQQQVYAQKHQQLQQMRMQQPP
Retrocopy NLGNLVIESKPAPGYTPNVVVGQVPTGTNHISKTPGQINL>AQLLLQHMQQQVYAQKHQQLQQMRMQQPP

Parental  APVPTTTTTTQQHPRQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQY
          APVPTTTTT.QQH..QAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQY
Retrocopy APVPTTTTT-QQHLKQAAPQMLQQQPPRLISVQTMQRGNMNCGAFQAHQMRLAQNAARIPGIPRHSGPQY

Parental  SMMQPHLQRQHSNPGHAGPFPVVSVHNTTINPTSPTTATMANANRGPTSPSVTAIELIPSVTNPENLPSL
          SMMQPHLQRQHSNPGHAGPFPVVSVHNT.INPTSPTTATMANAN.GPTSPSVTAIELIPSVTNPENLPSL
Retrocopy SMMQPHLQRQHSNPGHAGPFPVVSVHNTKINPTSPTTATMANAN*GPTSPSVTAIELIPSVTNPENLPSL

Parental  PDIPPIQV
          PDIPPIQ.
Retrocopy PDIPPIQL

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_706 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_706 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001716	1 retrocopy	retro_chof_534,
Ictidomys tridecemlineatus	ENSSTOG00000024757	1 retrocopy	retro_itri_706 ,