RetrogeneDB ID: retro_itri_1731

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393684.1:486115..487098(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000014702
• Aliases: None
• Description: None

Sequence

>retro_itri_1731
AGGCCAATGTGCAATACCAACATGTCTGTGTCTACTGATGGTGCTATAAGCACCTCACAGATTCCAGCTTCGGAACAAGA
GACCCTGGTTAGACCAAAGCCATTGCTTTTGAAGTTGTTAAAGTCTGTTGGTGCATAAAAAGACACTTATACTGTGAAAG
AGGTTATATTTTATCTTGGCCAGTATATTATGACTAAACTATTATATGATGAGAAGCAACAACATATTGTATATTGTTCA
AATTTCTAGGAGATTTGTTTGGAGTGCCAAGCTTCTTTGTGAAGGAGCACAGGAGAATATATACAATGATCTACAAAAAT
TTGGTGGTAGCCAATCAGGAGGAACCATCAGATTCCAGCACATTAGTGAGAACAGGTGTCACCTTGAAGGTGGGAGTGAT
CAGAAGGACCTTGTTCAAGAACTACAGGAAGGGAAGCCTTCATTTTCCTGTTTGGTTTCTAGACCATCTACCTCATCTAG
AAGGAGAGCAATTAGTGAGACAGAAGAAAATTCAGATGAATTATCTGGTGAATGATGAAAGTGCCACAAATCTGATAGTA
TTTTCCTTTCCTTTGATGAAAGCCTGCTCTGTGTGTAATAAGGGAAATATGTTGTGAAAGAAGCAGTAGCAGTGAATCAA
TAGAGAATCCATCAAATCCGGATATTGAAGATGGTGTGAGTGAAAATTCCAGTAATTGGTTGAATCAGGACTCAGTTTCA
GATCAATTTAGTGTAGAATTTGAAGTTGAATCTCTTGATTCAGAGGAAATAGCCTTAGTGAAGAAGGATAAGAACTCTCA
GATGAAGATGATGAGATATATCAAGTTATTGTGTATCAGGCAGGGGAAAGTGATATGGATTTATTTGAAGAAGATCCTGA
AATTTCTTTAGCTGACTATTTGAAGTGTACTTCGTGCAATGAAACGAATACTCCCCTTCCACCACATTGCAATAGATGTT
GGAACCTTAGTGAGAACTGGCTT

Alignment

ORF - retro_itri_1731 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.9 %
• Parental protein coverage: 67. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RPMCNTNMSVSTDGAVSTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVIFYLGQYIMTKRLYD
          RPMCNTNMSVSTDGA.STSQIPASEQETLVRPKPLLLKLLKSVGA.KDTYT.KEVIFYLGQYIMT..L..
Retrocopy RPMCNTNMSVSTDGAISTSQIPASEQETLVRPKPLLLKLLKSVGA*KDTYTVKEVIFYLGQYIMT-KLLY

Parental  EKQQHIVYCSNDL-LGDLFGVPSFSVKEHRKIYTMIYKNLVVVNQQEPSDSSTL-VKENRCHLEGGSDQK
          ...Q..........LGDLFGVPSF.VKEHR.IYTMIYKNLVV.N.QE....S.....ENRCHLEGGSDQK
Retrocopy DEKQQHIVYCSNF<LGDLFGVPSFFVKEHRRIYTMIYKNLVVAN-QEEPSDSST<ISENRCHLEGGSDQK

Parental  DLVQELQEEKPSSSCLVSRPSTSSRRRAISETDPEDNSDELSGERRKRHKSDSISLSFDESL-ALCVIRE
          DLVQELQE.KPS.SCLVSRPSTSSRRRAISET..E.NSDELSGE..K.HKSDSI.LSFDESL.ALCVIRE
Retrocopy DLVQELQEGKPSFSCLVSRPSTSSRRRAISET--EENSDELSGE**KCHKSDSIFLSFDESL<ALCVIRE

Parental  ICCERSSSSESIETPSNPDIEDGVSEHSSDWLDQDSVSDQFSVEFEVESLDSEDY-SLSEEGQELSDEDD
          ICCERSSSSESIE.PSNPDIEDGVSE.SS.WL.QDSVSDQFSVEFEVESLDSE...SLSEEG.ELSDEDD
Retrocopy ICCERSSSSESIENPSNPDIEDGVSENSSNWLNQDSVSDQFSVEFEVESLDSEEI<SLSEEG*ELSDEDD

Parental  EVYRVTVYQAGESDTDSFEEDPEISLADYWKCTSCNEMNPPLPPHCNRCWTLRENWL
          E.Y.V.VYQAGESD.D.FEEDPEISLADY.KCTSCNE.N.PLPPHCNRCW.L.ENWL
Retrocopy EIYQVIVYQAGESDMDLFEEDPEISLADYLKCTSCNETNTPLPPHCNRCWNLSENWL

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_1731 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1731 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004323	1 retrocopy	retro_cpor_1234,
Loxodonta africana	ENSLAFG00000005885	1 retrocopy	retro_lafr_715,
Otolemur garnettii	ENSOGAG00000034779	2 retrocopies	retro_ogar_1210, retro_ogar_49,
Ochotona princeps	ENSOPRG00000009677	1 retrocopy	retro_opri_891,
Ictidomys tridecemlineatus	ENSSTOG00000004184	1 retrocopy	retro_itri_428,
Ictidomys tridecemlineatus	ENSSTOG00000014702	1 retrocopy	retro_itri_1731 ,
Tupaia belangeri	ENSTBEG00000013758	2 retrocopies	retro_tbel_3216, retro_tbel_915,
Tarsius syrichta	ENSTSYG00000002908	2 retrocopies	retro_tsyr_1343, retro_tsyr_984,