RetrogeneDB ID: retro_itri_97

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393316.1:3026913..3028080(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000026225
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004651
• Aliases: None
• Description: None

Sequence

>retro_itri_97
ATGGACCACTTGGTGTGGACCAGCGGCCTCCTGGAGATCAACGAGACCCTGGTGATCCAGCAGCATGGGGTGCGCATCTA
CGACGGTGAGGAGAAGATAAAATTTGATGCTGGGACCCTCCTCCTTAGTACACACGGACTGATTTGGAGAGATCAGAAAA
ATCATGAGTGCTGCATGGCCATTCCTCTGTCCCACATTGTATTCATTGAGGAACAGGCAGCTGGAATTGGGAAGAGTGCC
AAAATAGTGGTTCATCTGTACCCAGCTCCTCCTACCAAAGAACCTGGCCCATTCCAGAGTAGTAAAAACTCCTATATCAA
ACTCTCCTTCAAAGAGCATGGCCAGATTGAGTTTTACAGGCGTTTATCAGAGGAAATGACACAAAGAAGATGGGAGAACA
TGCCAGTGTCTCAGTCAATACAAACAAATAGAGGACCCCAGCCAGGAAGAGTAAGAGCTGTAGGAATTGTAGGTATTGAA
AGGAAACTGGAAGAAAAAAGAAAAGAAACTGACAAAAATATTTCTGAGGCCTTTGAAGACCTCAGCAAGCTAATGATCAA
GGCTAAGGAAATGGTGGAGTTATCAAAATCAATTGCTAATAAAATTAAAGAGACGCAGGGTGACATCACAGAAGATGAGA
CCATCAGATTTAAGTCCTACTTGCTGAGCATGGGAATAGCTAACCCAGTTACCAGAGAAACCTATGGCTCAGGAACACAG
TACCACATGCAGCTGGCCAAACAGCTGGCTGGAATATTGCAGGTGCCTTTAGAGGAACGAGGCGGAATAATGTCACTCAC
ACTCACAGAGGTGTACTGTTTAGTAAACCGGGCTCGAGGAATGAAATTGCTCTCACCAGAAGATTTAGTGAATGCATGCA
AGATGCTAGAAGCACTGAAATTACCTCTCAGACTCCGGGTTTTTGACAGTAGCGTCATGGTAATTGAGCTTCAGTCCCAC
AAGGAAGAGGAAATGGTAGCCTCGGCCCTGGAGACAGTTTCAGAAAAAGGATCCCTAACATCAGAAGAGTTTGCCAAGCT
CTTGGGAATGTCTGTCCTCCTGGCCAAAGAAAGGTTACTGCTTGCAGAGAAGATGGGTCATCTTTGCCGAGATGACTCAG
TGGAAGGCTTGCCGTTTTACCCAAATTTATTTATGACACAGAGCTAA

Alignment

ORF - retro_itri_97 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IKFDAGTLLLSTHRLIWRDQKNHECCMAIPLSHIVFIEEQAAGIGKSAKIVVHLHPAPPTKEPGPFQSSK
          IKFDAGTLLLSTH.LIWRDQKNHECCMAIPLSHIVFIEEQAAGIGKSAKIVVHL.PAPPTKEPGPFQSSK
Retrocopy IKFDAGTLLLSTHGLIWRDQKNHECCMAIPLSHIVFIEEQAAGIGKSAKIVVHLYPAPPTKEPGPFQSSK

Parental  NSYIKLSFKEHGQIEFYRRLSEEMTQRRWENMPVSQSIQTNRGPQPGRVRAVGIVGIERKLEEKRKETDK
          NSYIKLSFKEHGQIEFYRRLSEEMTQRRWENMPVSQSIQTNRGPQPGRVRAVGIVGIERKLEEKRKETDK
Retrocopy NSYIKLSFKEHGQIEFYRRLSEEMTQRRWENMPVSQSIQTNRGPQPGRVRAVGIVGIERKLEEKRKETDK

Parental  NISEAFEDLSKLMIKAKEMVELSKSIANKIKEKQGDITEDETIRFKSYLLSMGIANPVTRETYGSGTQYH
          NISEAFEDLSKLMIKAKEMVELSKSIANKIKE.QGDITEDETIRFKSYLLSMGIANPVTRETYGSGTQYH
Retrocopy NISEAFEDLSKLMIKAKEMVELSKSIANKIKETQGDITEDETIRFKSYLLSMGIANPVTRETYGSGTQYH

Parental  MQLAKQLAGILQVPLEERGGIMS--LTEVYCLVNRARGMELLSPEDLVNACKMLEALKLPLRLRVFDSGV
          MQLAKQLAGILQVPLEERGGIMS..LTEVYCLVNRARGM.LLSPEDLVNACKMLEALKLPLRLRVFDS.V
Retrocopy MQLAKQLAGILQVPLEERGGIMSLTLTEVYCLVNRARGMKLLSPEDLVNACKMLEALKLPLRLRVFDSSV

Parental  MVIELQSHKEEEMVAAALETVSEKGSLTSEEFAKLVGMSVLLAKERLLLAEKMGHLCRDDSVEGLRFYPN
          MVIELQSHKEEEMVA.ALETVSEKGSLTSEEFAKL.GMSVLLAKERLLLAEKMGHLCRDDSVEGL.FYPN
Retrocopy MVIELQSHKEEEMVASALETVSEKGSLTSEEFAKLLGMSVLLAKERLLLAEKMGHLCRDDSVEGLPFYPN

Parental  LFMTQS
          LFMTQS
Retrocopy LFMTQS

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_97 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_97 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008949	1 retrocopy	retro_chof_702,
Macaca mulatta	ENSMMUG00000011360	1 retrocopy	retro_mmul_2510,
Otolemur garnettii	ENSOGAG00000011312	1 retrocopy	retro_ogar_913,
Ictidomys tridecemlineatus	ENSSTOG00000004651	1 retrocopy	retro_itri_97 ,