RetrogeneDB ID: retro_itri_891

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393338.1:10005631..10006425(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA1430
• Ensembl ID: ENSSTOG00000010864
• Aliases: None
• Description: KIAA1430 [Source:HGNC Symbol;Acc:29276]

Sequence

>retro_itri_891
ATAACTGCTTTATCAACTCCAGATATCAGCCCTGTTCCATCTTTTGAGTTAAATACACCAAATGACCAAAAAGTCAAAGT
TAAAAGGCAAGAAAATGTGAGTCAAGAGGTAGATGAAGATGTTGAGGTTTTAAAAATTGATTCAAGGTATCTGAAAGCAG
CCAAGAAAGTGAAAGAAAAACTTTGGCCTGCTGTTGTCCCAACGTCATCAGTGTTCAATTGTAATCTAGACCACAAAGTC
TTACATGTCACAATGAACCTGCATCATCTTTGAAAAGCTTTTCTGCAATTAAATAAAAAGGGACCACAAAAACTTCACTT
TGATCAACCCTCAGTAGTACCTAGGAAAAATTACTCTTTCACAAGAGAAGAGGTGAGACAGATTGATCAGGAAAATCAGA
GACTTTTGAAAGAACTGTCAAGGCAGGCTGAAAAGTCAGAAAGCAAAAGTACAATCCCCATTGATCATCCTTTTAAGTTA
TGTTGTAGTGCTCTCAATAGCCAGAAGGAGCAACAAAAGTTTGAAAGAGAAAATGTGGCTTTATTGAAAAAACTTGAAAC
TATGAAGCCAGCAATGGGTATGAAATACTCAGAACAGCTAATGGACTACCATTGTAATATGGGATCATCTCCTTCTAAGG
TCACCGTCCTCCAGAAGACTAAGAACATGCATTTGGCCAATGCATCCTATTAAGAGAAGTTTCCAGGACATCCAGTGCTA
ACAGCAGTGTCAGTTGTAAGACTGAGCAATTAGTTTTTGACACACCCAGTGGCCTATTGCTATGACTTAAACCC

Alignment

ORF - retro_itri_891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 50.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VTPLSTPDISPIQSFELGASNDQKIKVKRQENVSQEVYEDVEVLKNDSKHLKTARKGKEKCGPNLTPNSP
          .T.LSTPDISP..SFEL...NDQK.KVKRQENVSQEV.EDVEVLK.DS..LK.A.K.KEK..P...P.S.
Retrocopy ITALSTPDISPVPSFELNTPNDQKVKVKRQENVSQEVDEDVEVLKIDSRYLKAAKKVKEKLWPAVVPTSS

Parental  --DSDLDHRYKQKVLHDTMDLNHLLKAFLQLDKKVPQKHHFDQPSVVPRKNYSFTREEVRKIDRENQRLL
          .....LDH....KVLH.TM.L.HL.KAFLQL.KK.PQK.HFDQPSVVPRKNYSFTREEVR.ID.ENQRLL
Retrocopy VFNCNLDH----KVLHVTMNLHHL*KAFLQLNKKGPQKLHFDQPSVVPRKNYSFTREEVRQIDQENQRLL

Parental  KELSRQAEKPGSKSAIPRRSIGHPPKLYHSALNRQKEQQRIERENLALLKRLEAVKPTVGMKRSEQLMDY
          KELSRQAEK..SKS.IP...I.HP.KL..SALN.QKEQQ..EREN.ALLK.LE..KP..GMK.SEQLMDY
Retrocopy KELSRQAEKSESKSTIP---IDHPFKLCCSALNSQKEQQKFERENVALLKKLETMKPAMGMKYSEQLMDY

Parental  HRNMG-YLNATPPS-RQVRS-ALGQYSPLRGASRTSSATSGLSYKTERSAFDISSNPLLRPKP
          H.NMG..L....PS.R..R..A.GQ...LR..SRTSSA.S..S.KTE...FD..S..LL..KP
Retrocopy HCNMG>HLLLRSPSSRRLRT>AFGQCILLREVSRTSSANSSVSCKTEQLVFDTPSGLLL*LKP

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_891 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_891 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	ENSSTOG00000010864	1 retrocopy	retro_itri_891 ,