RetrogeneDB ID: retro_itri_1384

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393468.1:1789919..1790577(-)
• Located in intron of: ENSSTOG00000012121

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSSTOG00000012342
• Aliases: None
• Description: cytokine receptor-like factor 3 [Source:HGNC Symbol;Acc:17177]

Sequence

>retro_itri_1384
TGGAGCTTCACCACAAAGGCCTCACACAGACAACTGGAGAACTTACAGAAGTGCCTTTACTGGTTGATGTGCCTTGTTTA
TCTGCTTAGTTGGATGATTCAATTCTTAACATATTAAAGATAACATTTTGAAGCATGGAACAGTAGCATCTCTCCCACCA
GTGCAAATAGAAAAGCTAATAGAGAAACCTGAAGGCATCATAGAATGATGGCGTAAGGTGCATGACAATTTCGCAGACTA
AGATTACAGGCTTCAGTTCTGAAAATGCTCTTCAAAACATTTTGAAGATATATATGTAGATTCTGAAACTGAATTCATAG
TATTGCACATAGACCCCAAAGTTGATTATCAGTTCAGAGTCTGCACCTGAGAAGGTGTCCAACAAGAGTGGAGTCCATGG
AGCATCCCCCAAATAGGTCATTCTACGTTGGTGCCTCATGAGCAGACAACTGGCTTTGAGGGATATCACCTGAGCAGTCG
AAGAAATATAGCACTCTGGAATGATTCTGAATCCTCAGGTATACTCTACTCCAGCACTCCAACCTATATCTGTGGGCAGA
CATTAACATTCAGAGTTGAAACTGTGGGACAGCCAGACAGAAGAGATGGTATAGGAGTATGTGCAGAGAAGCAGAACATA
TATAACTCTGCAGCGAGA

Alignment

ORF - retro_itri_1384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.11 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WSFTKKASHIQLDSLP-EVPLLVDVPCLSAQLDDSILNI-VKDHIFKHGTVASRPPVQIEELIEKPGGII
          WSFT.KASH.QL..L..EVPLLVDVPCLSA.LDDSILNI..KD.I.KHGTVAS.PPVQIE.LIEKP.GII
Retrocopy WSFTTKASHRQLENLQ<EVPLLVDVPCLSA*LDDSILNI<IKDNILKHGTVASLPPVQIEKLIEKPEGII

Parental  VRWCKVDDDFTAQDYRLQFRKCSSNHFEDVYVGSETEFIVLHIDPNVDYQFRVCARGDGRQEWSPWSVPQ
          ..W.KV.D.F...DYRLQF.KCSS.HFED.YV.SETEFIVLHIDP.VDYQFRVC......QEWSPWS.PQ
Retrocopy E*WRKVHDNFAD*DYRLQF*KCSSKHFEDIYVDSETEFIVLHIDPKVDYQFRVCT*EGVQQEWSPWSIPQ

Parental  IGHSTLVPHEWTTGFEGYSLSSRRNIALRNDSESSGVLYSSAPTYICGQTLTFRQILVETVGQPDRRDSI
          IGHSTLVPHE.TTGFEGY.LSSRRNIAL.NDSESSG.LYSS.PTYICGQTLTFR...VETVGQPDRRD.I
Retrocopy IGHSTLVPHEQTTGFEGYHLSSRRNIALWNDSESSGILYSSTPTYICGQTLTFR---VETVGQPDRRDGI

Parental  GVCAEKQNGYDSLQR
          GVCAEKQN.Y.S..R
Retrocopy GVCAEKQNIYNSAAR

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_1384 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1384 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000017897	1 retrocopy	retro_etel_313,
Felis catus	ENSFCAG00000025986	1 retrocopy	retro_fcat_1916,
Macaca mulatta	ENSMMUG00000009069	2 retrocopies	retro_mmul_1002, retro_mmul_998,
Ictidomys tridecemlineatus	ENSSTOG00000012342	1 retrocopy	retro_itri_1384 ,