RetrogeneDB ID: retro_itri_270

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:20606608..20607003(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000016069
• Aliases: None
• Description: None

Sequence

>retro_itri_270
ATAAAAAACAAAATCCAAGCAAGCGTAGATCAGACATGCAGCCATTTAGAATAGCTGGAGTTTTTTTCCAGCAAGAAACT
CCCTAACAAAAGACAGAATGCCAAACATCAAGTCAACCAGTTAAAGTATGATGTCCATCACCTGCAGAATGCTCTCAGAA
ACTTCCAACATGGGCACTATGCTAGGGAGCAGCAGAAAAGACAGAGGAGTCTATCTCGAACACACCTTTACAACTAATGA
CTCTGACACCACCATACCAATGGACAGATCCCTGCAGTTTAACTCCTCCCTCCACACGTTCACCCCAGCATGGATGACTT
CATTGGAGGTGGGCACAGGATTCTAGAGGGACCAAGGACCAAAAACTGACCTTGAAGGACTCATAGAAATCCTTG

Alignment

ORF - retro_itri_270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.42 %
• Parental protein coverage: 62.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VENEIQASIDQIFSHLERLEILSSKEPPNKRQNAKLRVDQLKYDVQHLQTALRNFQQRRYAREQQ-ERQR
          ..N.IQAS.DQ..SHLE.LE..SSK..PNKRQNAK..V.QLKYDV.HLQ.ALRNFQ...YAREQQ.E...
Retrocopy IKNKIQASVDQTCSHLE*LEFFSSKKLPNKRQNAKHQVNQLKYDVHHLQNALRNFQHGHYAREQQ<EKTE

Parental  EEL-LSRTFTTNDSATTIPMDESLQFNSSLH-NIHHGMDDLIGGGHSILEGLRA-QRLTLKGTQKKI
          E...L..TFTTNDS.TTIPMD.SLQFNSSLH...H..MDD.IGGGH.ILEG.R..Q.LTLK...K..
Retrocopy ESI<LEHTFTTNDSDTTIPMDRSLQFNSSLH<HVHPSMDDFIGGGHRILEGPRT<QKLTLKDS*KSL

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_270 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_270 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013419	1 retrocopy	retro_cfam_1351,
Callithrix jacchus	ENSCJAG00000020030	1 retrocopy	retro_cjac_3180,
Felis catus	ENSFCAG00000028951	1 retrocopy	retro_fcat_678,
Myotis lucifugus	ENSMLUG00000002709	1 retrocopy	retro_mluc_752,
Macaca mulatta	ENSMMUG00000018689	1 retrocopy	retro_mmul_367,
Nomascus leucogenys	ENSNLEG00000004922	1 retrocopy	retro_nleu_1211,
Pongo abelii	ENSPPYG00000008290	1 retrocopy	retro_pabe_1596,
Pan troglodytes	ENSPTRG00000009323	1 retrocopy	retro_ptro_1290,
Ictidomys tridecemlineatus	ENSSTOG00000016069	2 retrocopies	retro_itri_1790, retro_itri_270 ,