RetrogeneDB ID: retro_itri_569

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393301.1:15252826..15253746(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SP2
• Ensembl ID: ENSSTOG00000015926
• Aliases: None
• Description: Sp2 transcription factor [Source:HGNC Symbol;Acc:11207]

Sequence

>retro_itri_569
ATGGTGCCCCCAAAGGAAGAGCAGCAGGAGATGGTGCAGATCCTCCAAGAGACTCTGCAGGGAGTGCAGACTGCACCCAC
TGCCCTCCCACCATCAGGCAAAAACCCTCCCAGAATTTTCAGATTCTGACTGCAGAGTCAGCGCCTACTCAGGTTGCCAC
TTGCACACCTTCCGGTAAAGGTACAGTCAGTTCTTGTTCAGGATAGCCTCTTAGCAATAGCTGCAACCACCTCAACAACC
ATATGTAGCAGCCCTGCACACCAAGCTCCCTAGCTGAATGGGACCAGCAGAAAACAGTTTGATTCAATTCTCCCAAAAGA
GCATCCCTACTACAGATTGAGCCTGTTGGGAGAGTCATCATTCTGAACACACCACAGCAGCTGCCCAGGCAATGCAGACC
ATCAATATCAACCAAGTCCAAGTCCAGGGCATGCTGTCACCATCACCAACACTAGCCAGACAGCAGCAATTATAAGTGCA
GAATGTTTCTGGAAACAACTTGACCATCGGTGAGCTAAGCCCCAACTAGATCCAGCTGCAGAAGGAGGAGGTCCTAGCCA
GAGATGCCCCACCTGGGGAGAAGTGCTGTATGGCCTACATGAGTCCCAATTGCAAAGATGGGGAGAAGAGGTCTGGAGAC
AGGGCCAGAAAAAGCATGTGTCCATATCCCTGACTGTGGCAAGACTTTTCTGAAGGCATCTCTGCTGCAGGCCCACTGGC
AACTACACACCAGCAAGCTGCTCTTGCTCTGCAAATGGTTCTTCTATGGAAAGAAGTTCACATGGAGAGACAAGCTCCAG
AGGCACACTCTCATCCACACAGAAGACAAACACTTTTGAGTGCACCCAGGGTCAGAAGTGCTTCATGAAAAGTGACCACC
TTACCAAGCATTACAAGATCCACCTGTCCCAAAGAACTTA

Alignment

ORF - retro_itri_569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.8 %
• Parental protein coverage: 50.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  VVPPKAEQQQVVQIPQQALRVVQAASATLP-TVPQKPSQNFQIQTAESTPTQVYIRTPSGE-VQTVLVQD
          .VPPK.EQQ..VQI.Q..L..VQ.A...LP.T..QKPSQNFQI.TAES.PTQV...TPSG..VQ.VLVQD
Retrocopy MVPPKEEQQEMVQILQETLQGVQTAPTALP<TIRQKPSQNFQILTAESAPTQVATCTPSGK>VQSVLVQD

Parental  SPPATAATTSTTTCSSPAPRAPHLSGTSKKHSAAILRKERP-LPKIAPAGSIISLNAAQ-LAAAAQAMQT
          S..A.AATTSTT.CSSPA..AP.L.GTS.K....IL.KE.P.L..I.P.G..I.LN..Q..AA.A..MQT
Retrocopy SLLAIAATTSTTICSSPAHQAP*LNGTSRKQFDSILPKEHP<LLQIEPVGRVIILNTPQ<AAAQA--MQT

Parental  ININGVQVQGV-PVTITNT-GGQQQLTVQNVSGNNLTISGLSPTQIQLQMEQALAGEAQPGEKRRRMACT
          ININ.VQVQG...VTITNT...QQQL.VQNVSGNNLTI..LSP..IQLQ.E..LA..A.PGEK...MA..
Retrocopy ININQVQVQGM<AVTITNT>ARQQQL*VQNVSGNNLTIGELSPN*IQLQKEEVLARDAPPGEK-CCMAYM

Parental  CPNCKDGEKRSGE-QGKKKHV-CHIPDCGKTFRKTSLLRAHVRLHTGERPFVCNWFFCGKRFTRSDELQR
          .PNCKDGEKRSG..QG.KKHV..HIPDCGKTF.K.SLL.AH..LHT......C.WFF.GK.FT..D.LQR
Retrocopy SPNCKDGEKRSGD<QGQKKHV<VHIPDCGKTFLKASLLQAHWQLHTSKLLLLCKWFFYGKKFTWRDKLQR

Parental  HARTHTGDKR-FECAQCQKRFMRSDHLTKHYKTHL-VTKNL
          H...HT.DK..FEC.Q.QK.FM.SDHLTKHYK.HL.V.KNL
Retrocopy HTLIHTEDKH>FECTQGQKCFMKSDHLTKHYKIHL<VPKNL

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_569 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_569 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013740	1 retrocopy	retro_btau_1617,
Ictidomys tridecemlineatus	ENSSTOG00000015926	1 retrocopy	retro_itri_569 ,
Ictidomys tridecemlineatus	ENSSTOG00000022002	1 retrocopy	retro_itri_1862,