RetrogeneDB ID: retro_itri_1348

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393448.1:1642210..1642689(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020921
• 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_1348
GTTTTTAGGAATCAACTATCCAGGAAAAATAAGTTTTACTCCTATGAGCCATCTTCTGAGAACCCTTTCCCAGAATCAGA
ACCTGTGTGTCTCCAACTTAAGTCGGGTGCTCATCTCTGCAGGGTTTGTGGCTCTTAGGCCCCAAAACGTGTTCCAGATG
CCGCCAAGCACACTACTGCAGTAAGGAGCATCAGACGCTGGACTGGAGGTTGGAGCACAAGCAGCCTTGTACCCAAGGTC
ATTTGGACCATACAGTTCCAGGCCACAACTTCCTTTTTCTTGAATTCGAAATTGTCATAGAAACAGAGGAGGAGATTGTG
CCTGAAGTTGTGAAAAAGGAAGAAGACTTTGAGATCACAGGAAGCACGGATGAAGCTCTTGAGGGAGAACTGGATTCCAT
GGGAAAGCATGAATCCAGGGAAAATAACATTTTCCAGAAGTTCAAAGCTCAGATAGCCCTTGAACCAGAGCAGGTCATG

Alignment

ORF - retro_itri_1348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.42 %
• Parental protein coverage: 64.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VFRNQLPRKNEFYSYEPPSENPSPETESVCLQLKSGAHLCRVCGC-LGPKTCSRCHQAHYCSKEHQTLDW
          VFRNQL.RKN.FYSYEP.SENP.PE.E.VCLQLKSGAHLCRVCG..LGPKTCSRC.QAHYCSKEHQTLDW
Retrocopy VFRNQLSRKNKFYSYEPSSENPFPESEPVCLQLKSGAHLCRVCGS<LGPKTCSRCRQAHYCSKEHQTLDW

Parental  RLGHKQACTQVDHLDHTVPDHNFLFPEFEIVIETEEEIVPEVVEKEEDFEITGSMDEALEEELDSMAKHE
          RL.HKQ.CTQ..HLDHTVP.HNFLF.EFEIVIETEEEIVPEVV.KEEDFEITGS.DEALE.ELDSM.KHE
Retrocopy RLEHKQPCTQ-GHLDHTVPGHNFLFLEFEIVIETEEEIVPEVVKKEEDFEITGSTDEALEGELDSMGKHE

Parental  SREDNIFQKFKAQIALEPEQIL
          SRE.NIFQKFKAQIALEPEQ..
Retrocopy SRENNIFQKFKAQIALEPEQVM

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_1348 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1348 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 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,