RetrogeneDB ID: retro_itri_1719

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393660.1:338921..339193(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DESI1
• Ensembl ID: ENSSTOG00000009480
• Aliases: None
• Description: desumoylating isopeptidase 1 [Source:HGNC Symbol;Acc:24577]

Sequence

>retro_itri_1719
CAGATTACAGAAGAAATCTTTCTGGAGTACCTGTCCTCCCTGAGGGAGTCTCTGTTCGGAGGTGAAACCTATAACCTCTT
TGAACACAACTGTAACACCTTCAGCAAGAAGTGGCACAGTTTCTGACTGGGCGGAAAATCCCTTCTTACATCACTGACCT
GCCCTCTGATGTTCTCTCCACGCCCTTCGGACAGGCACTCCGACCGCTCCTGGACTCCATCCAGATCCAGCCTCCTGGAG
GGAACACTGTGGGCAGACCCAATGGCCAGAGC

Alignment

ORF - retro_itri_1719 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.22 %
• Parental protein coverage: 54.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EVTEEIFLEYLSSLGESLFRGEAYNLFEHNCNTFSN-EVAQFLTGRKIPSYITDLPSEVLSTPFGQALRP
          ..TEEIFLEYLSSL.ESLF.GE.YNLFEHNCNTFS..EVAQFLTGRKIPSYITDLPS.VLSTPFGQALRP
Retrocopy QITEEIFLEYLSSLRESLFGGETYNLFEHNCNTFSK<EVAQFLTGRKIPSYITDLPSDVLSTPFGQALRP

Parental  LLDSIQIQPPGGNAVGRPNGQS
          LLDSIQIQPPGGN.VGRPNGQS
Retrocopy LLDSIQIQPPGGNTVGRPNGQS

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_1719 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1719 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018941	1 retrocopy	retro_cjac_1874,
Echinops telfairi	ENSETEG00000005136	1 retrocopy	retro_etel_2107,
Monodelphis domestica	ENSMODG00000016577	2 retrocopies	retro_mdom_1548, retro_mdom_684,
Ictidomys tridecemlineatus	ENSSTOG00000009480	1 retrocopy	retro_itri_1719 ,