RetrogeneDB ID: retro_itri_1635

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393597.1:740331..740826(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000026171
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSSTOG00000022768
• Aliases: None
• Description: programmed cell death 2 [Source:HGNC Symbol;Acc:8762]

Sequence

>retro_itri_1635
GTTTTTAGGAATCAGCTACCCAGGAAAAATGAGTTTTACTCCTATGAGCCACCATCAGAGAACCCTTCCCCAGAAACAGA
ATCTGTGTGTCTCCAACTTAAGTCGGGCGCTCACCTCTGCAAGGTTTGTGGCTGTTTAGGCCCTAAAACGTGTTCCAGAT
GCCACCGAGCACACTACTGCACTAAGGAGCATCAGACGCTAGACTGGAGGTGGATGCACAAGCAGGCTTGTACCCAAGAT
CATTTGGACCATACAGTTCCAGACCACAACTTCCTTTTTCCTGAATTCGAAATTGTCATAGAAACAGAGGAGGAGATTGT
GCCTGAAGCTGTGGAAAAGGAAGAAGACTTTGAGATCACAGGAAGCATGGACGAAGCTCTTGAGGAAGAACTGGATTCCA
TGGCAAAGCATGAATCCAGGGAAGATAACATTTTCCAGAAGTTCAAAGCTCAGATAGCCCTTGAACCAGAGCAGATGCTC
AGTTACGGCAGGGGT

Alignment

ORF - retro_itri_1635 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.58 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFRNQLPRKNEFYSYEPPSENPSPETESVCLQLKSGAHLCRVCGCLGPKTCSRCHQAHYCSKEHQTLDWR
          VFRNQLPRKNEFYSYEPPSENPSPETESVCLQLKSGAHLC.VCGCLGPKTCSRCH.AHYC.KEHQTLDWR
Retrocopy VFRNQLPRKNEFYSYEPPSENPSPETESVCLQLKSGAHLCKVCGCLGPKTCSRCHRAHYCTKEHQTLDWR

Parental  LGHKQACTQVDHLDHTVPDHNFLFPEFEIVIETEEEIVPEVVEKEEDFEITGSMDEALEEELDSMAKHES
          ..HKQACTQ.DHLDHTVPDHNFLFPEFEIVIETEEEIVPE.VEKEEDFEITGSMDEALEEELDSMAKHES
Retrocopy WMHKQACTQ-DHLDHTVPDHNFLFPEFEIVIETEEEIVPEAVEKEEDFEITGSMDEALEEELDSMAKHES

Parental  REDNIFQKFKAQIALEPEQILRYGRG
          REDNIFQKFKAQIALEPEQ.L.YGRG
Retrocopy REDNIFQKFKAQIALEPEQMLSYGRG

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_1635 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1635 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Cavia porcellus	ENSCPOG00000002920	1 retrocopy	retro_cpor_168,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,
Ictidomys tridecemlineatus	ENSSTOG00000022768	2 retrocopies	retro_itri_1348, retro_itri_1635 ,