RetrogeneDB ID: retro_itri_1124

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393381.1:4312354..4312767(-)
• Located in intron of: ENSSTOG00000016450

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOP16
• Ensembl ID: ENSSTOG00000004869
• Aliases: None
• Description: NOP16 nucleolar protein [Source:HGNC Symbol;Acc:26934]

Sequence

>retro_itri_1124
TGCCCCCTTTTTCTCCATGCTTGTGACCACACCAAATTGATGAGACAGAAGCTGGCCAAGATGAATTGGCCAATGATCCC
TATGAAGGTGGTGCCTCTCCATAAGAGAAAGGTGAAGGCCATGGAATCAAGCGTGGAGAAGAGTCCTAGGGGCTTGTGTA
GAAACCCATGTACAAAATGACATGGAGGCAAAGCCAGCATCCAGAGAAGAAAGAAAATATCCTGTCTTAGGACCTCATTG
AGTACATACAATACATGGTGGAGAGCCATGGGGAGGCCTTGGCTGGGAATGTGAAGAATTGCTATCAGGATACTCTGAAA
CACATTGGGAAGATCAATGTCTATAAATGTTTTTACCCAGCAGAGTGGCAAGCCTTCATCGATTCTTCACAGAAGAATAA
GGTGGAGGGTGAG

Alignment

ORF - retro_itri_1124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.82 %
• Parental protein coverage: 80.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CSHIRHAWDHAKSVRQNLAEMGLAMDPNKAVPLRKKKAMGMDIDVEERPKELVR-KP-YVLNDLEAE-AS
          C....HA.DH.K..RQ.LA.M...M.P.K.VPL.K.K...M...VE..P..L.R.KP..V.ND.EA..AS
Retrocopy CPLFLHACDHTKLMRQKLAKMNWPMIPMKVVPLHKRKVKAMESSVEKSPRGLCR<KP<HVQNDMEAK<AS

Parental  L-PEKKGNTLSRDLIDYVRYMVENHGEDYKAMARDEKNYYQDTPKQIRNKINVYKRFYPAEWQTFIDSLQ
          ..PEKK.N.LS.DLI.Y..YMVE.HGE...A.A...KN.YQDT.K.I..KINVYK.FYPAEWQ.FIDS.Q
Retrocopy I<PEKKENILS*DLIEYIQYMVESHGE---ALAGNVKNCYQDTLKHI-GKINVYKCFYPAEWQAFIDSSQ

Parental  KNKMEVE
          KNK.E.E
Retrocopy KNKVEGE

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_1124 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1124 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016694	2 retrocopies	retro_cfam_1790, retro_cfam_1793,
Callithrix jacchus	ENSCJAG00000012315	1 retrocopy	retro_cjac_2208,
Echinops telfairi	ENSETEG00000010391	1 retrocopy	retro_etel_1329,
Mustela putorius furo	ENSMPUG00000012552	1 retrocopy	retro_mputfur_381,
Otolemur garnettii	ENSOGAG00000000824	2 retrocopies	retro_ogar_1323, retro_ogar_2299,
Rattus norvegicus	ENSRNOG00000017284	1 retrocopy	retro_rnor_2739,
Sus scrofa	ENSSSCG00000029577	1 retrocopy	retro_sscr_510,
Ictidomys tridecemlineatus	ENSSTOG00000004869	1 retrocopy	retro_itri_1124 ,