RetrogeneDB ID: retro_itri_1110

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393377.1:6582353..6582689(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R14B
• Ensembl ID: ENSSTOG00000021959
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14B [Source:HGNC Symbol;Acc:9057]

Sequence

>retro_itri_1110
GGGGTCCCAGGTGAGCGCCTGGGTGGTGCTGGCAACTAGTGCCCAGGGAGACGCCAAGGGAAAGTCACTGTCAGGTAAGC
CCCAAAGCTGCTGCGAAGCGCCTCAACTTGGAGGAATGGACCTTGGGACAGCTCCCAAGCCCTACCACTGCCAGGAAGAG
AAGACCCCAGAGCTGCAGATTGGCGTGGACCAGCTCTGGACATGGAAAGCAATGATACCCAGGCTGCCAGAGTCAAGGAG
CTGATGGTTGGCTGTTACAAACCCACTGACGCCTTCATCCCCGCCCTGCTGGACAAGATGCAGGACATGCAGAAGCTGAG
CTCACCCCAGGAGGAG

Alignment

ORF - retro_itri_1110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.79 %
• Parental protein coverage: 79.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAAGEGPGGADDEGPVRRQGKVTVKYDRKELR-KRLNLEEWILEQLT-RLYDCQEEEIPELEIDVDEL-L
          G..GE..GGA....P.RRQGKVTV....K.LR.KRLNLEEW.L.QL....Y.CQEE..PEL.I.VD.L.L
Retrocopy GVPGERLGGAGN*CPGRRQGKVTVR*APKLLR<KRLNLEEWTLGQLP<KPYHCQEEKTPELQIGVDQL<L

Parental  DMETDDTRAARVKELLVDCYKPTEAFISGLLDKIRGMQKLSTPQKK
          DME..DT.AARVKEL.V.CYKPT.AFI..LLDK...MQKLS.PQ..
Retrocopy DMESNDTQAARVKELMVGCYKPTDAFIPALLDKMQDMQKLSSPQEE

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_1110 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1110 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 7 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018111	3 retrocopies	retro_cjac_3591, retro_cjac_428, retro_cjac_532,
Homo sapiens	ENSG00000173457	4 retrocopies	retro_hsap_2205, retro_hsap_3101, retro_hsap_3655, retro_hsap_3838,
Mustela putorius furo	ENSMPUG00000013208	2 retrocopies	retro_mputfur_235, retro_mputfur_798,
Nomascus leucogenys	ENSNLEG00000004890	2 retrocopies	retro_nleu_324, retro_nleu_335,
Pan troglodytes	ENSPTRG00000041138	6 retrocopies	retro_ptro_1674, retro_ptro_2097, retro_ptro_2480, retro_ptro_2614, retro_ptro_3089, retro_ptro_935,
Sus scrofa	ENSSSCG00000013035	2 retrocopies	retro_sscr_1087, retro_sscr_892,
Ictidomys tridecemlineatus	ENSSTOG00000021959	1 retrocopy	retro_itri_1110 ,