RetrogeneDB ID: retro_itri_907

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393341.1:1428757..1429622(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000027590
• Aliases: None
• Description: None

Sequence

>retro_itri_907
AAAATGATTGTGATAGAGCAAGCAGAGGCCTAGCTCTCTTAGTTAGACCTGCTGGCCAGTATTTTTCCTGGGGATAATGA
GCTCATAGTGAATGACCAACTGGCTTTAGCAGAACTGAAAGATCGTATTGGAAAGAAGACTATGGAGGGGCGATCTTCAA
AAGTTTACTATACCATCAACATAAACCTAGACATATCTGAGAAATCAATGGAGATATGTTCTGTGGCCTGCATTCTTCCC
TTTAAGTACCCTGAAGTTCTGCCTGAAATTACTGCCAGATCAGTATTATTAAGTAGAACCCAGCAGACCCAGCTGAACAC
AGATCTGACCGCATTCCTGCAGGAGAATTGTGGAGGAGATGTCTGTATATTGAATGCCACAGAATAAGTTAGAGAACAGG
CTGTCAGCAGAGATGCCCCATCTTCTCCCACCACAGAAAGTATAGTCCAGCTTGTTGATCCCATTCTTACAAGACTTTGG
ATCTATAGCCATAACATCTATAACAGATGCAAAAGAAAGAATAGTCTAGAGTGGGCCAAGGAGCTTTCCCTGTCTGGGTT
TAGCATGCCTGGAAAACCTGGTGTTGTTTATGTGGAAAGTCCACAAAGTGCCTGGGAAGAATTCTGGTCCAGACTCAGAA
AATTAAACTGGAAGAGAATCTTAATCTGCCATCAAGAAGACATTCCTTTTGATGGTACAGATGATGAAATGGAAAGACAA
AGAAGATTTTCCATTTTTGAAGAAAAAGTGTTCAGTGTTAATGGAGCCAGAGGAAACCACATGGATATTGGTTATATGTA
TCAGTTCTTAAATGCCAAAGGCTGTGGGGATGTTTTCCAGATGTTTTTTGGTGTTAGAAGGACAG

Alignment

ORF - retro_itri_907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.64 %
• Parental protein coverage: 97.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMTEIEQAEAQLSELDLLASMFPGENELIVNDQLALAELKDCIEKKTMEERSSKVYYTINMNLDISEKSM
          KM..IEQAEA.LS.LDLLAS.FPG.NELIVNDQLALAELKD.I.KKTME.RSSKVYYTIN.NLDISEKSM
Retrocopy KMIVIEQAEA*LS*LDLLASIFPGDNELIVNDQLALAELKDRIGKKTMEGRSSKVYYTININLDISEKSM

Parental  EIFSLACILPFKYPEVLPEITVRSVLLSRSKQTQLNTDLTAYLQENCQGDVCILNATEWVREHASGYVSK
          EI.S.ACILPFKYPEVLPEIT.RSVLLSR..QTQLNTDLTA.LQENC.GDVCILNATE.VRE.A...VS.
Retrocopy EICSVACILPFKYPEVLPEITARSVLLSRTQQTQLNTDLTAFLQENCGGDVCILNATE*VREQA---VSR

Parental  DVPSSPTTESAVQPVDPILTRLWIYSHHIYNKCKRKNILEWAKELSLSGFSMPGKPGVVCVEGPQSACEE
          D.PSSPTTES.VQ.VDPILTRLWIYSH.IYN.CKRKN.LEWAKELSLSGFSMPGKPGVV.VE.PQSA.EE
Retrocopy DAPSSPTTESIVQLVDPILTRLWIYSHNIYNRCKRKNSLEWAKELSLSGFSMPGKPGVVYVESPQSAWEE

Parental  FWSRLRKLNWKRILIRHREDIPFDGTNDEMERQRRFSIFEEKVFSVNGARGNHMDFGQLYQFLNAKGCGD
          FWSRLRKLNWKRILI.H.EDIPFDGT.DEMERQRRFSIFEEKVFSVNGARGNHMD.G..YQFLNAKGCGD
Retrocopy FWSRLRKLNWKRILICHQEDIPFDGTDDEMERQRRFSIFEEKVFSVNGARGNHMDIGYMYQFLNAKGCGD

Parental  VFQMFFGV-EGQ
          VFQMFFGV.EGQ
Retrocopy VFQMFFGV>EGQ

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_907 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_907 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000004504	1 retrocopy	retro_lafr_547,
Ictidomys tridecemlineatus	ENSSTOG00000027590	1 retrocopy	retro_itri_907 ,