RetrogeneDB ID: retro_itri_1410

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393480.1:3259296..3260096(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYA
• Ensembl ID: ENSSTOG00000023405
• Aliases: None
• Description: nuclear transcription factor Y, alpha [Source:HGNC Symbol;Acc:7804]

Sequence

>retro_itri_1410
GGCCAACCTATTATAGCCAAGGCTGTCCCTGGGGGACAAGGTCAAACCATCATGCAAGTAACTGTATCTGGGACACAGGG
TTTGTAACAGATACAACTGGTTCTACCTGGACAGATCCAAATCCAGGGTGGGCAGGCTGTGCAGGTCCAGAGCCAGCAAG
GTCAGACCCAGCAGATCATCATTCAGCAGCCTCAGACAGCTGTCACTGCTGGCCAGACTCAGACTCAGCAACAAATTGCT
GTCCAGGGAAAGCAAGTGGCACAGACTGCTGAAGGGAAAACCATTATCTACCAGCCAGTTAATGCAGATGGTAGTATTCT
CCAGCAAGGCGTGATCACCATCCCATTAGTCAGTTTGGCAGGAGCACAGATTGTTCTGACAGGAGCCAATACCAACACTT
CCAGGGACAAGGGGCTGTCACTGTTACATTAGCAGTGGTAGGCAATGTGGTCAATTCCAGAGGGATGGTCATGATGCTGC
CTGGAGCTGGCTCTGTGCCTGCTCTCCAGAGAATCCCCCTACGTGGAGCAGAGATGCTTGAAGAAGAGCCCCTCTATGTG
AATGCCAAACAGTACCACCATATTCTTAAAAAGAGGCAAGCTCAGGAAAAACTAGAAGCAGAAGGGAAAATTCCAAAGGA
AAGAAGGAAATACTTGCATGAGTCTCAGCAGCCTCATGCCATGGCTCAGATGTGTGGTAAAGGTGGACGATTTTTCTCTC
CCAAAGAAAAGGATAGTCCCCATATGCAGGATCCAAACCAAACTGATGAAGAAGAAATGACACAGATAATTGGAGTCTCC

Alignment

ORF - retro_itri_1410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.71 %
• Parental protein coverage: 75.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GQTIMQVPVSGTQGLQQIQLV---PPGQIQIQGGQAVQVQGQQGQTQQIIIQQPQTAVTAGQTQTQQQIA
          GQ.I....V.G.QG....Q.......G..QIQ.....Q.Q.Q.GQ..Q...QQ.QT.....Q.......A
Retrocopy GQPIIAKAVPGGQGQTIMQVTVSGTQGL*QIQLVLPGQIQIQGGQAVQVQSQQGQTQQIIIQQPQTAVTA

Parental  VQGQQVAQTAEGQTIVYQPVNADGTILQQVTVPVS----GMITIPAASLAGAQIVQTGANTNTTS-SGQG
          .Q.Q...Q.A.....V.Q.......I.Q.V....S....G.ITIP..SLAGAQIV.TGANTN.TS..GQG
Retrocopy GQTQTQQQIAVQGKQVAQTAEGKTIIYQPVNADGSILQQGVITIPLVSLAGAQIVLTGANTN-TS<QGQG

Parental  TVTVTLPVAGNVVNSGGMVMMVPGAGSVPAIQRIPLPGAEMLEEEPLYVNAKQYHRILKRRQARAKLEAE
          .VTVTL.V.GNVVNS.GMVMM.PGAGSVPA.QRIPL.GAEMLEEEPLYVNAKQYH.ILK.RQA..KLEAE
Retrocopy AVTVTLAVVGNVVNSRGMVMMLPGAGSVPALQRIPLRGAEMLEEEPLYVNAKQYHHILKKRQAQEKLEAE

Parental  GKIPKERRKYLHESRHRHAMARKRGEGGRFFSPKEKDSPHMQDPNQADEEAMTQIIRVS
          GKIPKERRKYLHES...HAMA...G.GGRFFSPKEKDSPHMQDPNQ.DEE.MTQII.VS
Retrocopy GKIPKERRKYLHESQQPHAMAQMCGKGGRFFSPKEKDSPHMQDPNQTDEEEMTQIIGVS

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_1410 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1410 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
Ailuropoda melanoleuca	ENSAMEG00000004435	1 retrocopy	retro_amel_1701,
Bos taurus	ENSBTAG00000009905	1 retrocopy	retro_btau_676,
Ictidomys tridecemlineatus	ENSSTOG00000023405	1 retrocopy	retro_itri_1410 ,