RetrogeneDB ID: retro_itri_159

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393629.1:16898..17282(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000026134
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PPP1R11
• Ensembl ID: ENSSTOG00000003632
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 11 [Source:HGNC Symbol;Acc:9285]

Sequence

>retro_itri_159
ATGGAAGATACAGCATCTATGCTGACAGAAGTCATATCAGAGCCCACAATTACACTGGAAAATGAAGTGAAGTGTAGCAA
TCTGTCCACTCCTCTACAGAAGGGAAAATCAGACAAGAGAGTGGAATGGTCAAGTGATACAATAGACAATGAGCACTTGG
GCCGTCGCTCATCTAAATGCTGTTGCATTTATGAGAAGCCTCGTGCATTTGGTGAAAGTTCCTCTGAGAGTGAAAAAGAA
GATGAAGAGAACTGTGATGCTATACTATGTATCTGGGGTCATCACAGGGGAAGGCGTCGTACCCTTTCCAATAGTGCTTC
TAGTACTTCATCTTCAAAACCTCCAGACCCACGTCAACCCCTTCCTTCACCCATTAAGGGTTAA

Alignment

ORF - retro_itri_159 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.59 %
• Parental protein coverage: 99.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEAGAGLSETVTETTVTVTTEPENRSLTIKLRKRKPEKKVEWTSDTVDNEHMGRRSSKCCCIYEKPRAF
          M......L.E...E.T.T...E.....L...L.K.K..K.VEW.SDT.DNEH.GRRSSKCCCIYEKPRAF
Retrocopy MEDTASMLTEVISEPTITLENEVKCSNLSTPLQKGKSDKRVEWSSDTIDNEHLGRRSSKCCCIYEKPRAF

Parental  GESSTESEDEDEEGCGHSHCVRGHRKGRSHA-TPGPTPTTPPQPPDPSQPPPGPMQ
          GESS.ESE.EDEE.C....C..GH..GR..........T....PPDP.QP.P.P..
Retrocopy GESSSESEKEDEENCDAILCIWGHHRGRRRTLSNSASSTSSSKPPDPRQPLPSPIK

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_159 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_159 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020710	1 retrocopy	retro_cjac_2880,
Felis catus	ENSFCAG00000013592	1 retrocopy	retro_fcat_1794,
Gorilla gorilla	ENSGGOG00000026830	1 retrocopy	retro_ggor_80,
Macropus eugenii	ENSMEUG00000006493	2 retrocopies	retro_meug_715, retro_meug_933,
Macaca mulatta	ENSMMUG00000012122	1 retrocopy	retro_mmul_359,
Monodelphis domestica	ENSMODG00000016021	1 retrocopy	retro_mdom_98,
Nomascus leucogenys	ENSNLEG00000004933	1 retrocopy	retro_nleu_2257,
Otolemur garnettii	ENSOGAG00000001598	1 retrocopy	retro_ogar_1458,
Pongo abelii	ENSPPYG00000029642	1 retrocopy	retro_pabe_492,
Pan troglodytes	ENSPTRG00000017915	1 retrocopy	retro_ptro_2969,
Pteropus vampyrus	ENSPVAG00000008330	1 retrocopy	retro_pvam_894,
Ictidomys tridecemlineatus	ENSSTOG00000003632	1 retrocopy	retro_itri_159 ,