RetrogeneDB ID: retro_itri_1495

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393510.1:683280..683559(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000022867
• Aliases: None
• Description: None

Sequence

>retro_itri_1495
CCTGTTTCTGATGACTGTAGATATACTATTAACAGCTTGGTGGCTTACCTGCTGCACATCAGTGATGCCTATTTATCCAT
GGCCTGCTACTATATTGATGAGAAAGAATGCCTCCTTTTGTCATGTTCTTGGAGGAACAAGCTGGGTTAAAGAGGCAACA
AGCAAAGCATTTCCCAAGATTTCTAAGAAAACAGACAGTATGATCTGCCTTTGGTTATGAAGAGACCAGATGTAGATAAC
TGGGGAAGTGTCACCCAAGCACTGACATCTGCTCTGCAG

Alignment

ORF - retro_itri_1495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.04 %
• Parental protein coverage: 54.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PVPEECRYQINHVASYLMHISDIYLSMACYYVDQK-GMPPFVMFFEEEAELKRQQAKHFLRFLRKR-NST
          PV...CRY.IN....YL.HISD.YLSMACYY.D.K..MPPFVMF.EE.A.LKRQQAKHF.RFLRK...S.
Retrocopy PVSDDCRYTINSLVAYLLHISDAYLSMACYYIDEK<RMPPFVMFLEEQAGLKRQQAKHFPRFLRKQ<DSM

Parental  ICL-PVIERSDIDNWGSAMQALTSAVQ
          ICL..V..R.D.DNWGS..QALTSA.Q
Retrocopy ICL<LVMKRPDVDNWGSVTQALTSALQ

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_1495 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1495 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015497	1 retrocopy	retro_amel_333,
Canis familiaris	ENSCAFG00000028564	9 retrocopies	retro_cfam_1158, retro_cfam_1163, retro_cfam_1432, retro_cfam_1901, retro_cfam_365, retro_cfam_448, retro_cfam_567, retro_cfam_715, retro_cfam_746,
Ictidomys tridecemlineatus	ENSSTOG00000022867	1 retrocopy	retro_itri_1495 ,