RetrogeneDB ID: retro_itri_1356

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393455.1:3034747..3035732(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000027265
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJB11
• Ensembl ID: ENSSTOG00000009449
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily B, member 11 [Source:HGNC Symbol;Acc:14889]

Sequence

>retro_itri_1356
CTGGGGGTACCTCGAAGTGCCTCTATAAAGGATATTAAGAAGGCCTACAGGAAACTAGCCCTGCAGCTTCATCCTGACCA
GAACCCTGATGATCCCCAAGCCCAGGAGAAATTCCAGGATCTGGGTGCTGCTTATGAGGTTCTGTCACATAGTGAAAAAT
GGAAACAATATGATACATATGGTGAAGAAAGGATCGAAAGATGGTCATCAGAGCTCCCATGGAGACATTTTTTCGCACAT
TTTTGGAGATTTTGGTTTCATGTTTGGAGGAACCCCTCGCCAGCAAGACAGAAATATTCCAAGAGGAAGTGATATTATCG
TAGATCTAGAAGTCACTTTGGAAGAAGTATATGCTGGAAATTATGTGGAAGTAGTTAGAAATAAACCTGTGGCAAGGCAG
GCTCCTGGCAAACGGAAATGCAACTGTCGGCAAGAAATGGGGACCACCCAGCTGGGCCCAGGTCGCTTCCAGATGACCCA
AGAGGTAGTCTGCGATGAGTGTCCTAATGTTAAATTAGTGAATGAAGAACGAACGCTGGAAGTAGAAATAGAACCTGGAG
TGAGAGATGCCATGGAGTACCCCTTTATTGGAGAAGGTGAGCCTCATGTGGATGGTGAGCCTGGAGACTTACGCTTCCGA
ATCAAAGTTGTCAAGCACCGGATATTTGAAAGGAGAGGAGATGATTTGTACACCAATGTGACAATCTCACTAGTTGAGTC
TCTAGTCGGCTTTGAGATGGATATTACTCACTTGGATGGTCACAAGGTACATATTTCCCGGGATAAGATCACCAGGCCAG
GAGCCAAGCTATGGAAAAAGGGGGAAGGGCTCCCTAACTTTGACAACAACAGTATCAAGGGCTCTTTAATAATCACATTT
GATGTGGATTTTCCAAAACAATTAACAGAGGAAGCAAGAGAAGGTATCAAACAGCTACTGAAACAAGGATCAGTGCAGAA
AGGATACAATGGACTGCAAGGATAT

Alignment

ORF - retro_itri_1356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.66 %
• Parental protein coverage: 91.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGVPRSASIKDIKKAYRKLALQLHPDRNPDDPQAQEKFQDLGAAYEVLSDSEKRKQYDTYGEE-GLKDGH
          LGVPRSASIKDIKKAYRKLALQLHPD.NPDDPQAQEKFQDLGAAYEVLS.SEK.KQYDTYGEE.G.KDGH
Retrocopy LGVPRSASIKDIKKAYRKLALQLHPDQNPDDPQAQEKFQDLGAAYEVLSHSEKWKQYDTYGEE>GSKDGH

Parental  QSSHGDIFSHFFGDFGFMFGGTPRQQDRNIPRGSDIIVDLEVTLEEVYAGNFVEVVRNKPVARQAPGKRK
          QSSHGDIFSH.FGDFGFMFGGTPRQQDRNIPRGSDIIVDLEVTLEEVYAGN.VEVVRNKPVARQAPGKRK
Retrocopy QSSHGDIFSHIFGDFGFMFGGTPRQQDRNIPRGSDIIVDLEVTLEEVYAGNYVEVVRNKPVARQAPGKRK

Parental  CNCRQEMRTTQLGPGRFQMTQEVVCDECPNVKLVNEERTLEVEIEPGVRDGMEYPFIGEGEPHVDGEPGD
          CNCRQEM.TTQLGPGRFQMTQEVVCDECPNVKLVNEERTLEVEIEPGVRD.MEYPFIGEGEPHVDGEPGD
Retrocopy CNCRQEMGTTQLGPGRFQMTQEVVCDECPNVKLVNEERTLEVEIEPGVRDAMEYPFIGEGEPHVDGEPGD

Parental  LRFRIKVVKHRIFERRGDDLYTNVTISLVESLVGFEMDITHLDGHKVHISRDKITRPGAKLWKKGEGLPN
          LRFRIKVVKHRIFERRGDDLYTNVTISLVESLVGFEMDITHLDGHKVHISRDKITRPGAKLWKKGEGLPN
Retrocopy LRFRIKVVKHRIFERRGDDLYTNVTISLVESLVGFEMDITHLDGHKVHISRDKITRPGAKLWKKGEGLPN

Parental  FDNNNIKGSLIITFDVDFPKQLTEEAREGIKQLLKQGSVQKVYNGLQGY
          FDNN.IKGSLIITFDVDFPKQLTEEAREGIKQLLKQGSVQK.YNGLQGY
Retrocopy FDNNSIKGSLIITFDVDFPKQLTEEAREGIKQLLKQGSVQKGYNGLQGY

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_1356 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1356 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000004007	1 retrocopy	retro_itri_343,
Ictidomys tridecemlineatus	ENSSTOG00000005200	4 retrocopies	retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,
Ictidomys tridecemlineatus	ENSSTOG00000009449	1 retrocopy	retro_itri_1356 ,