RetrogeneDB ID: retro_itri_474

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393294.1:2171529..2172416(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000008617
• Aliases: None
• Description: None

Sequence

>retro_itri_474
CTAGAGAACCTGGGGCTGACCTATGTCAATGGTATCAACAGTGGGGATCTGCCCTGCAAGGAGAATGCAGTCCTGGCCCT
GGCCCAGAGAGAAAATTCAGCTGCAGTATAAAAGGCACTTGCCCACTATGACCAGCTGATGGGCCAGAAGGTGCAGCTGC
CCACAGAGACCCTCCAGGAGCTGCTGGAAATGCACAGGGCCAGTGAAAGAGAGGCCATAGAAATCCTCACAAAGAACTGG
TTCCAGGATGAGGACCAAAGTTTCCAGAAGGAATTACAGACCCTACTAGATGCAAAGCAGAAAGACATTTGTAAACAGAA
TGAAGAAGCCTCTTCAGATTGCTCAGCTTTCTTCAGGATATTTCTGGTCCTCTGGAAGAAGCAGTGAAGCAAGGGCTTTA
TTCTAAACCAAGAGGCCATGATGTCTACCTTCAGAAGACTGAGAAGCTGAAGACAAAGTTCCATCAGCAGCCCAGGAAAG
GAACACAAGCTGAGGAAGCTCTGCAAAAGAATTTAAAGTCCAAAGAGTCTGTGAGTAACTCTGTTCTACAGACAGTCCTG
GCTCTCACAGCCAAGGAAAACGAGATGAAAGAGGCATGTGCAATAACAGAGGCTGCCAAGGCTGAAGCAGAAAGTGTGGA
GGTGATTCGTAGACATGCAGCAAATGATGAAAGAGAAGGAGAGACTCCATCAGCAGCAAATAAGACTATAGAGATAGAAA
GAGCAAACTGTTTGGCACAGCAACAGTTGGAGCAGGAACATCATCTGCAGGAAGAAGCCAAAAAGCTCAGGTTGATCCAT
CAAGCTGAAATGTCAAGGTTTCAAGATCAGATCCAGCATATCCATGGAACAATGTCTGAGCCACAAGCTGCTTGATGTAT
CATACTC

Alignment

ORF - retro_itri_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.09 %
• Parental protein coverage: 50.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LESLVLTYVNAINSGDLPCLENAVLALAQRENAAAIKRALAHYDQLMGQKVQLPTDTLQELLGLHRASER
          LE.L.LTYVN.INSGDLPC.ENAVLALAQREN.AA...ALAHYDQLMGQKVQLPT.TLQELL..HRASER
Retrocopy LENLGLTYVNGINSGDLPCKENAVLALAQRENSAAV*KALAHYDQLMGQKVQLPTETLQELLEMHRASER

Parental  EAIKIFTENSFKDEDQSFQKELKTLLDAKQNDICKQNEEVSSDRCSA-LLQDIFGPLEEAVKQGVYSKPG
          EAI.I.T.N.F.DEDQSFQKEL.TLLDAKQ.DICKQNEE.SSD.CSA..LQDI.GPLEEAVKQG.YSKP.
Retrocopy EAIEILTKNWFQDEDQSFQKELQTLLDAKQKDICKQNEEASSD-CSA<FLQDISGPLEEAVKQGLYSKPR

Parental  GHNLYLQKTEELKAKYHQQPRKGIQAKKALQKYLKSKESVSKAVLQTDQALTAKEKEMKEARIKAEAAKA
          GH..YLQKTE.LK.K.HQQPRKG.QA..ALQK.LKSKESVS..VLQT..ALTAKE.EMKEA....EAAKA
Retrocopy GHDVYLQKTEKLKTKFHQQPRKGTQAEEALQKNLKSKESVSNSVLQTVLALTAKENEMKEACAITEAAKA

Parental  EAERLQAIRR-QQQQMIEERERLHRQQIR-QMEIDKANFQAQQQREQERRLQEEAQRLKLIHQAQISRFQ
          EAE....IRR..QQ.M..E.ERLH.QQIR...EI..AN..AQQQ.EQE..LQEEA..L.LIHQA..SRFQ
Retrocopy EAESVEVIRR>MQQ-MMKEKERLHQQQIR<TIEIERANCLAQQQLEQEHHLQEEAKKLRLIHQAEMSRFQ

Parental  AQIQQLQSTRPQPQPDPCLIL
          .QIQ....T...PQ...C.IL
Retrocopy DQIQHIHGTMSEPQAA*CIIL

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_474 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_474 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000008617	1 retrocopy	retro_itri_474 ,