RetrogeneDB ID: retro_itri_30

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393365.1:2134508..2136392(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000005500
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TKTL1
• Ensembl ID: ENSSTOG00000005014
• Aliases: None
• Description: transketolase-like 1 [Source:HGNC Symbol;Acc:11835]

Sequence

>retro_itri_30
ATGGCCATGGCCAACGACGCCAAGCCCGACGCCGAGACGCTGCAGGTGCTGCAGGACATGGCCCACCGCCTGCGAATCCA
CTCCATCAGGGCCACGTGTGCCTGCAGCTCCGGGCACCCCACGTCGTGCTGCAGTGCCGCGGAGATCATGTCGGTGCTCT
TCTTCTACGCCATGAGGTACAAAGGGACCGAGCCGGAGCACCGCGACAACGACCGGTTTGTCCTCTCCAAGGGCCACGCG
GCTCCAATCCTCTACGCCGCTTGGGCCGAGATAGGCGACATCCGCGAATCCGACTTGCTGAGCTTGAGGAAAATCCACTG
CGACTTGGAGGGCCACCCCACGCCTCGACTCTCGTTTGTGGACGTGGCAACAGGGTCCCTGGGGCAAGGACTAGGCGCTG
CCTGTGGAATGGCGTACACGGGCAAGTACTTCGACAAGGCCAGCTACCGGGTGTTCTGCCTCATGGGAGATGGCGAATCC
TCAGAAGGCTCTGTCTGGGAGGCTTTGGCTTTTGCTTCCCACTACAGTTTGGACAATCTCGTGGCAGTCTTCGACGTGAA
CCGCTTGGGACAAAGTGGCACTGCCCCCCTGGAGCACTGCACAGACATCTATCAGAGTCGCTGCGAAGCCTTTGGATGGA
ATACCTACCTAGTGGATGGTCATGATGTGGAGGCCTTGTGCCACGCATTTTGGCAAGCAGCTCAAGTGAAGAACAGACCT
ACTGCTGTCATCGCCAAGACCTTCAAGGGTCGAGGTATTCCAAACATTGAGGATGCAGAAAATTGGCATGGAAAGCCAAT
GCCCAAAGAGAGAGCAGATGCAATTATCCAGTTAATTGAGAGTCAGATACAGACCAACAGGAATCTCATGCCCCAGCCCC
CTGTGGAAGACTCACCTCCGATCAGCATCACTAATATAAAAATGACCTCTCCGCCTTCTTACAAAGCTGGTGACAAGATA
GCTACTCGGAAAGCATGTGGTCTGGCTCTGGCTAAGCTAGGCCATGCACATGAAAGAGTTATTGTTCTGGATGGTGACAC
AAAGAACTCCACCTTTTCTGAGATATTCAAGAAAGAACACCCTGAGCGTTTCATAGAGTGTTTTATTGCTGAGCAAAACA
TGGTTAGTGTGGCACTGGGCTGTGCCACACGTGGTCGTACCATTGCCTTTGCTAGTACCTTTGCTGCCTTTTTGACCCGA
GCATTTGATCAGATCCGAATGGGAGCCATCTCCCAAACTGATATCAACCTCATTGGTTCTCACTGTGGAGTATCCGTCGG
TGAAGATGGACCATCTCAGATGGCCCTAGAAGACCTAGCCATGTTTCGGAGTATTCCCAATTGCACCATTTTCTATCCAA
GTGATGCTATATCAACAGAGCATGCTGTTTATCTGGCTGCCAATACCAAGGGCATGTGCTTCATTAGAACCACCCGACCA
GAAACTGCAATCATTTATACTGCACAAGAAAATTTTGAGATTGGACAGGCCAAGGTAGTCCGCCACAGTGTTAATGACAA
GGTTACAGTTATTGGAGCTGGAGTTACTCTACACGAAGCCTTAGCAGCTGCTGATGATCTTTCTCAACAAGGTATTTCTA
TCCGTGTCATTGACCCATTTACTATTAAACCCCTGGATACAGCCACTATTATTTCCAGTGCAAAAGCCACAGGTGGCCGG
GTTATCACAGTAGAAGATCACTACAGAGAAGGTGGTATTGGAGAAGCAGTCTGTGCAGCTGTCTCCAGGGAGCCTGGCAT
CCTTGTTCATCAGCTGGCAGTGACAGAAGTGCCTCGAAGTGGGAAACCCAGTGAATTGCTGGACATGTTTGGAATCAGTG
CCAAACAAATCATAGAGGCTGTGAAATATACTTTAATGAGCTAA

Alignment

ORF - retro_itri_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.2 %
• Parental protein coverage: 83.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLGSLGPRLSFVDVATGWLGQGLGAACGMAYTGKYFDQASYRVFCLLGDGESSEGSVWEALAFASYYSLD
          L.G...PRLSFVDVATG.LGQGLGAACGMAYTGKYFD.ASYRVFCL.GDGESSEGSVWEALAFAS.YSLD
Retrocopy LEGHPTPRLSFVDVATGSLGQGLGAACGMAYTGKYFDKASYRVFCLMGDGESSEGSVWEALAFASHYSLD

Parental  NLVVIFDVNRLGHGGTLPLEHCIEVYQKRCEAFGWNTYVVDGRDVEALCQVFWQAAQVKSKPTAVVAKTF
          NLV..FDVNRLG..GT.PLEHC...YQ.RCEAFGWNTY.VDG.DVEALC..FWQAAQVK..PTAV.AKTF
Retrocopy NLVAVFDVNRLGQSGTAPLEHCTDIYQSRCEAFGWNTYLVDGHDVEALCHAFWQAAQVKNRPTAVIAKTF

Parental  KGRGMPNVEDAENWYGKPMPKERADAIIKLIESQIQTNRSLLPQPPIEDSPQVNIMDIKMTCPPAYEVGD
          KGRG.PN.EDAENW.GKPMPKERADAII.LIESQIQTNR.L.PQPP.EDSP...I..IKMT.PP.Y..GD
Retrocopy KGRGIPNIEDAENWHGKPMPKERADAIIQLIESQIQTNRNLMPQPPVEDSPPISITNIKMTSPPSYKAGD

Parental  VVATRKACGLALAKLGHANNRVIVLDGDTKNSTFSEIFKKEHPERFIECFIAEQNMVSVALGCATRGRTI
          ..ATRKACGLALAKLGHA..RVIVLDGDTKNSTFSEIFKKEHPERFIECFIAEQNMVSVALGCATRGRTI
Retrocopy KIATRKACGLALAKLGHAHERVIVLDGDTKNSTFSEIFKKEHPERFIECFIAEQNMVSVALGCATRGRTI

Parental  AFASTFAAFLTRAFDQIRMGAIAQININLIGSHCGVSVGEDGPSQMALEDLAMFRAVPNCTIFYPSDAVS
          AFASTFAAFLTRAFDQIRMGAI.Q..INLIGSHCGVSVGEDGPSQMALEDLAMFR..PNCTIFYPSDA.S
Retrocopy AFASTFAAFLTRAFDQIRMGAISQTDINLIGSHCGVSVGEDGPSQMALEDLAMFRSIPNCTIFYPSDAIS

Parental  TEHAIYLAANTKGMCFIRTSRPETAVLYTPQETFKIGQAKVVRQSVNDKVTVIGAGITLHEALVAADDLS
          TEHA.YLAANTKGMCFIRT.RPETA..YT.QE.F.IGQAKVVR.SVNDKVTVIGAG.TLHEAL.AADDLS
Retrocopy TEHAVYLAANTKGMCFIRTTRPETAIIYTAQENFEIGQAKVVRHSVNDKVTVIGAGVTLHEALAAADDLS

Parental  KQDIFIRVIDLFTIKPLDVATIISNARATGGRIITVEDHYPEGGIGEAVSAAVSMEPDILVHQLAVMGVP
          .Q.I.IRVID.FTIKPLD.ATIIS.A.ATGGR.ITVEDHY.EGGIGEAV.AAVS.EP.ILVHQLAV..VP
Retrocopy QQGISIRVIDPFTIKPLDTATIISSAKATGGRVITVEDHYREGGIGEAVCAAVSREPGILVHQLAVTEVP

Parental  RSGRPSELLDTFGISARHIIVAVKCMLMN
          RSG.PSELLD.FGISA..II.AVK..LM.
Retrocopy RSGKPSELLDMFGISAKQIIEAVKYTLMS

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_30 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_30 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018441	1 retrocopy	retro_amel_119,
Equus caballus	ENSECAG00000021992	1 retrocopy	retro_ecab_6,
Felis catus	ENSFCAG00000011392	1 retrocopy	retro_fcat_84,
Loxodonta africana	ENSLAFG00000005145	1 retrocopy	retro_lafr_6,
Pongo abelii	ENSPPYG00000020870	1 retrocopy	retro_pabe_205,
Ictidomys tridecemlineatus	ENSSTOG00000005014	1 retrocopy	retro_itri_30 ,