RetrogeneDB ID: retro_itri_1319

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393440.1:1505648..1506867(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WASF1
• Ensembl ID: ENSSTOG00000005949
• Aliases: None
• Description: WAS protein family, member 1 [Source:HGNC Symbol;Acc:12732]

Sequence

>retro_itri_1319
GAAGAAGAAGAATTGTCTTTGCAGGACATAACAATGAGAAAAGCCTTCCGAAGTTCTACAATTCAAGATCAGCAGCTTTT
CGACTGCAAGACTTTGCCTATTCCATTTCAAGAGACATAAGATGTTTGTGAACAACCTCCACCTCTCAACATACTTACTC
CTTATAGAGATGATGGTAAAGAAGGTTTGAAGTTTTCATACCAATCCTTCATATTTCTTTGATCTGTGGAAAGAAAAAAT
GTTGCAAGATACAGAGGACAAGAGGAAGGAAAAGAGGAAACAGAAGCAGAAAAATCTAGATCGTCCTCATGAACCAGAAA
AAGTGCCAAGAGCACCTCATGACAGGAGGAGAGAATGGCAGAAGCTGGCCCAAGGTCCAGAGCTGGCTGAAGATGATGCT
AATCTCTTATATAAGCATACTGAAGTTACTAATGGCCCGGCCTCTCGTTTTGAAACAAGACCTCAGACTTACGTGGATCA
TATGGATGGATCTTATTCACTTTCTGCCTTGCCATTTAGTCAGATAAGTGAGCTTCTGACTAGAGCTGAGGAAAGGGTCT
TAGTCAGACCACATGAACCACCTCCGCCTCCACCCATGCATGGAACAGGAGATGCAAAACCCATACCCACCTGTATCAGT
TCTGCTACAGGTTTGATAGAAAATCACCCTCAGTCACCAGCCACAGGCAGAACACCTGTGTTTGTGAGCCCCACTCCCCC
ACCTCCTCCACCTCCTCTTCCATCTGTCTTGTCAACTTCTTCATTAAGAGCTTCAATGACTTCCACTCCTCCCCCAGTAC
CTCTCCCACTTCCACCTCCAACCACTGCTTTGCAAGCTCCAGTTGTACCACCACCTCCAGCTCCTCTTCAGATTGCGCCT
GGAATTCTTCACCCAGCTCCTCCTCCATTTGCACCTCCTCTAGTACAACCCTCTCCACCAGTAGCTAGAGCTGCCCTAGT
ATGTGAAACTGTACCAGTTCATCCACTCCCACAAGGTGAAGTCCAGGGGCTGCCTCCACCCCCACCACCGCCTCCTCTGC
CTCCACCTGGCATTCGACCATCATCAGCTGTCACAGTTGCAGCTCTTGCTCATCCTCCCTCTGGGCTACATCCAACACCA
TCTACTGCCCCAGGTCCCCATGTTCCATTAATGCCTCCATCTCCTCCATCACAACTTATACCTGCTTCTGAACCAAAGTG
TCATCCATCAACCCTACCT

Alignment

ORF - retro_itri_1319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.4 %
• Parental protein coverage: 72.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEEELSLQDITMRKAFRSSTIQDQQLFDRKTLPIPLQETYDVCEQPPPLNILTPYRDDGKEGLKF-YTNP
          .EEELSLQDITMRKAFRSSTIQDQQLFD.KTLPIP.QET.DVCEQPPPLNILTPYRDDGKEGLKF..TNP
Retrocopy EEEELSLQDITMRKAFRSSTIQDQQLFDCKTLPIPFQET*DVCEQPPPLNILTPYRDDGKEGLKF>HTNP

Parental  SYFFDLWKEKMLQDTEDKRKEKRKQKQKNLDRPHEPEKVPRAPHDRRREWQKLAQGPELAEDDANLLHKH
          SYFFDLWKEKMLQDTEDKRKEKRKQKQKNLDRPHEPEKVPRAPHDRRREWQKLAQGPELAEDDANLL.KH
Retrocopy SYFFDLWKEKMLQDTEDKRKEKRKQKQKNLDRPHEPEKVPRAPHDRRREWQKLAQGPELAEDDANLLYKH

Parental  IEVANGPASHFETRPQTYVDHMDGSYSLSALPFSQMSELLTRAEERVLVRPHEPPPPPPMHGTGDAKPIP
          .EV.NGPAS.FETRPQTYVDHMDGSYSLSALPFSQ.SELLTRAEERVLVRPHEPPPPPPMHGTGDAKPIP
Retrocopy TEVTNGPASRFETRPQTYVDHMDGSYSLSALPFSQISELLTRAEERVLVRPHEPPPPPPMHGTGDAKPIP

Parental  TCISSATGLIENRPQSPATGRTPVFVSPTPPPPPPPLPSALSTSSLRASMTSTPPPPVPPPPPPPTTALQ
          TCISSATGLIEN.PQSPATGRTPVFVSP.........PS.LSTSSLRASMTST.PPPVP.P.PPPTTALQ
Retrocopy TCISSATGLIENHPQSPATGRTPVFVSPXXXXXXXXXPSVLSTSSLRASMTST-PPPVPLPLPPPTTALQ

Parental  APAVPPPPAPLQIAPGVLHPAPPPIAPPLVQPSPPVARAAPVCETVPVHPLPQGEVQGLPPPPPPPPLPP
          AP.VPPPPAPLQIAPG.LHPAPPP.APPLVQPSPPVARAA.VCETVPVHPLPQGEVQGLPPPPPPPPLPP
Retrocopy APVVPPPPAPLQIAPGILHPAPPPFAPPLVQPSPPVARAALVCETVPVHPLPQGEVQGLPPPPPPPPLPP

Parental  PGIRPSSAVTVAALAHPPSGLHPTPSTAPGPHVPLMPPSPPSQVIPASEPKRHPSTLP
          PGIRPSSAVTVAALAHPPSGLHPTPSTAPGPHVPLMPPSPPSQ.IPASEPK.HPSTLP
Retrocopy PGIRPSSAVTVAALAHPPSGLHPTPSTAPGPHVPLMPPSPPSQLIPASEPKCHPSTLP

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_1319 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1319 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
Equus caballus	ENSECAG00000022222	1 retrocopy	retro_ecab_343,
Otolemur garnettii	ENSOGAG00000008623	1 retrocopy	retro_ogar_895,
Ictidomys tridecemlineatus	ENSSTOG00000005949	1 retrocopy	retro_itri_1319 ,