RetrogeneDB ID: retro_itri_1729

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393684.1:262429..262895(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT7
• Ensembl ID: ENSSTOG00000009175
• Aliases: None
• Description: CCR4-NOT transcription complex, subunit 7 [Source:HGNC Symbol;Acc:14101]

Sequence

>retro_itri_1729
GGAGGAAAGACTCAGTACTTTGCAGAACTTCTTGTGACTTCCAGAGTGGTTCTCTATGAAGGCGTCAATTGATAATCATT
TCTCAGTGGCTAGGACTTTGGCAATTTAATAAAAATCCTGACCAACTATAATTTGCCCAAAGAAGAACATGACTTCTTTG
AGATTCTTTCAATTGTACTTCTCCTGTTATTTATGATGTGAATACTTCAAGGAGAACTGAGAAAAATCTTAACAGTGGAT
TACAAGAGTTCTGAACAGCTAGAGCTGAAACAGGTAGGACATAACATCAGGCAGGATCAAATTTGTTGTTTTCAACAATG
GTCTTTTTCAAAAAGAGAGAAATGTTCTTTGAAGATCATATCAGTGAGACAGATATTATGGTCATTTGTGTGGCCGCGAT
CCTAGTTCATTCCATGTACAAAGTGGCACAGGGAATGCATAGGAAGAGGAAGCCAACAAGCAGTCA

Alignment

ORF - retro_itri_1729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.33 %
• Parental protein coverage: 54.74 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLM
          G..TQYFAELL.TS.VVL.EGV...SF.SG.DFG.LIKILTN.NLP.EE.DFFEIL............L.
Retrocopy GGKTQYFAELLVTSRVVLYEGVN**SFLSG*DFGNLIKILTNYNLPKEEHDFFEILSIVLLLLFMM*ILQ

Parental  KSCKNLKGGLQEVAEQLELERIGPQ-HQAGSDSLLTGMAFFKMREMFFEDHIDDA-KYCGHLYGLGSGSS
          ..............EQLEL...G...HQAGS..L...M.FFK.REMFFEDHI.....Y.GHL.G....S.
Retrocopy GELRKILTVDYKSSEQLELKQVGHN<HQAGSNLLFSTMVFFKKREMFFEDHISET<RYYGHLCGRDPSSF

Parental  YVQNGTGNAYEEEANKQS
          .VQ.GTGNA.EEEANKQS
Retrocopy HVQSGTGNA*EEEANKQS

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_1729 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1729 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720,
Felis catus	ENSFCAG00000000591	1 retrocopy	retro_fcat_1889,
Homo sapiens	ENSG00000198791	2 retrocopies	retro_hsap_211, retro_hsap_4851,
Macaca mulatta	ENSMMUG00000001873	1 retrocopy	retro_mmul_2592,
Mustela putorius furo	ENSMPUG00000017972	1 retrocopy	retro_mputfur_1596,
Nomascus leucogenys	ENSNLEG00000002489	2 retrocopies	retro_nleu_1860, retro_nleu_2373,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118,
Otolemur garnettii	ENSOGAG00000006324	2 retrocopies	retro_ogar_1883, retro_ogar_505,
Pongo abelii	ENSPPYG00000018385	2 retrocopies	retro_pabe_3771, retro_pabe_428,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631,
Ictidomys tridecemlineatus	ENSSTOG00000009175	2 retrocopies	retro_itri_1729 , retro_itri_1730,