RetrogeneDB ID: retro_itri_677

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393310.1:8253340..8254211(+)
• Located in intron of: ENSSTOG00000028147

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPA1
• Ensembl ID: ENSSTOG00000022475
• Aliases: None
• Description: replication protein A1, 70kDa [Source:HGNC Symbol;Acc:10289]

Sequence

>retro_itri_677
TCCAAAGTGATACCCATTGCCAGCCCACCTCTTACCAGTCCAAGTGGACTATTTATGCTCATGTTAGCAACAAAAGTCAA
ATCTGTACCTGGAGCAATTCGAGGAGAAGTAAACTTTTCTCTATAGAACTAGTTGTTAAAAGTGGTAAAATCAAAGCTGC
TACTTTCAGTTGGCAAGTAGACAAGTTCTTTCTCCTTACTGAAGTTAAGAAGATGTATTATTTCTCAAAATGCACCCCGA
AGATCGCTAACAAATAATTTTCTGCTGTTAAAAATGACTATGAGATGACTTTCAATGAGACTTGTGTCATGCCCTGTGAA
GATGATCATCATCTACCTACAGTTCAGTTTGATTTCACTGACATCGGTGACTTAGAGAACAAGTCTAAAGACACACTTGT
AGACATAATCGGGATCTGCAAGAGCTATACAGATGCTTCTAAAATCACAATAAAATTTAACAACAGAGAAGTTTCTAAAA
GAAATATCTATTTAATGGACATGTCAGGGAAAGTGGTGACTGCTACTCTATGGAGAGAAGATGCTGACAAGTTTGATGGT
TCTAGACATCCTGTGATGGCCATTAAAGGAGCCAGAGTTTTCCATTTTGGAGGACAGAACATTTCCGTACTATCTGAATT
CAAGCACTGTCATTTTGAACCCTGACATTTCAGAGGCCTATAAGCTTTGTGGATGGTTGGACTCAGAAGAACAAGCCTTA
GATGTTTCCTCTCTAATCTAAAGAGTGGAGAAAAAAGAGAAGGCAACACCAACCGGAAAACCTTATATGAGGTTAAATCA
GAGAACTTGGGCCATGGTGACAACGCCGACTATTTAGCTCTGTGGCAATGGTGGTGTCTTTGCAAAGAGAA

Alignment

ORF - retro_itri_677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.5 %
• Parental protein coverage: 59.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SKVVPIASL-TPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSIELVDESGEIRATAFNEQVDKFFPLIE
          SKV.PIAS..T.YQSKWTI.A.V.NKSQI.TWSNSR...KLFSIELV..SG.I.A..F..QVDKFF.L.E
Retrocopy SKVIPIASP<TSYQSKWTIYAHVSNKSQICTWSNSR-RSKLFSIELVVKSGKIKAATFSWQVDKFFLLTE

Parental  VNKVYYFSKGTLKIANKQFSAVKNDYEMTFNNETSVMPCEDDHHLPTVQFDFTGIGDLENKPKDSLVDII
          V.K.YYFSK.T.KIANK.FSAVKNDYEMTFN.ET.VMPCEDDHHLPTVQFDFT.IGDLENK.KD.LVDII
Retrocopy VKKMYYFSKCTPKIANK*FSAVKNDYEMTFN-ETCVMPCEDDHHLPTVQFDFTDIGDLENKSKDTLVDII

Parental  GICKSYEDATKITVKSTNREVSKRNIYLMDMSGKVVNATLWGEDADKFDGSRQPVMAIKGARVSDFGGRS
          GICKSY.DA.KIT.K..NREVSKRNIYLMDMSGKVV.ATLW.EDADKFDGSR.PVMAIKGARV..FGG..
Retrocopy GICKSYTDASKITIKFNNREVSKRNIYLMDMSGKVVTATLWREDADKFDGSRHPVMAIKGARVFHFGGQN

Parental  LSILS-SSTIIV-NPDIPEAYKLRGWFDSEGQALDGVS-ISDLKSGGVGGSNTNWKTLYEVKSENLGQGD
          .S.LS..S.....NPDI.EAYKL.GW.DSE.QALD.VS..S.LKSG.....NTN.KTLYEVKSENLG.GD
Retrocopy ISVLS>NSSTVILNPDISEAYKLCGWLDSEEQALD-VS<LSNLKSGEKREGNTNRKTLYEVKSENLGHGD

Parental  KADY-FSSVATVVYLRKE
          .ADY.FSSVA.VV.L..E
Retrocopy NADY<FSSVAMVVSLQRE

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_677 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_677 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013540	2 retrocopies	retro_chof_167, retro_chof_2578,
Rattus norvegicus	ENSRNOG00000003123	1 retrocopy	retro_rnor_1373,
Ictidomys tridecemlineatus	ENSSTOG00000022475	1 retrocopy	retro_itri_677 ,