RetrogeneDB ID: retro_itri_1736

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393699.1:384713..385451(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT7
• Ensembl ID: ENSSTOG00000021378
• Aliases: None
• Description: septin 7 [Source:HGNC Symbol;Acc:1717]

Sequence

>retro_itri_1736
TATTCCTCACATCTGTATTCTCCAGAGTATCTAGGTCCTTCCCATAGAATAAAAAAGGCTGGGCAGTGGAACAATCCAAA
CTTTTCACCAAAGAAGGTGGTGTTCAGTTGCTGTTCATAATATTTGTTACCCTAAGGATTTAGAGATGCAGTGGATAATA
GTAATTACTGGAAGCCTGTTATTGACTAAATTTTAAGTAAATTTTAAGATTACCTAAATGCAGAATCTCAAGTAAACAGA
CATCAGATGCCTGATAACAGAGTGAAGTGTTGTTTATACTTCGTTGCTCCTTTAGGACATAGACTTAAACCATTGGATAT
TGAGTTTATGAAACGTTTGCATGAAAAAGTAAATATCATCCCACTATTGCCAAAGCAGACACACTCACACCCAAGGAATG
CCAACAGTTTAAAAAACAGATAATGAAAGAAATTGGGGAAAATAAAATATATGAATTTCCAGAATCAGATGATGAAGAAG
AAAATAAGCAGGTTAAAAAGAAAAAGGACCATTTACCTCTTGCTGTGGTAGGTAGTAATATTATCATTAAAGTTAATGGC
AAAAGGGTCAGAGGAAGGCAGTATCCTTGGGGTATGGCTGAAATTGAATATGGTAAACATTGTGATTTTACAATTCTAAG
AAATATGTTGATAATAACACACATGCAGGACTTGAAAGATGTTACACAGTAATGTACACCATGAGAACTACAGAAGCAGA
AAATTGGCAGCTGTAACT

Alignment

ORF - retro_itri_1736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 59.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FLTDLYSPEYPGPSHRIKKTVQ-VEQSKVLIKEGGVQLLLTIVDTP-GFGDAVDNSNCWQPVIDYIDSKF
          ....LYSPEY.GPSHRIKK..Q.VEQSK...KEGGVQLL..I..T..GF.DAVDNSN.W.PVID.I.SKF
Retrocopy YSSHLYSPEYLGPSHRIKKAGQ<VEQSKLFTKEGGVQLLFIIFVTL>GFRDAVDNSNYWKPVID*ILSKF

Parental  EDYLNAESRVNRRQMPDNRVQCCLYFVAPSGHGLKPLDIEFMKRLHEKVNIIPL-IAKADTLTPEECQQF
          .DYLNAES.VNR.QMPDNRV.CCLYFVAP.GH.LKPLDIEFMKRLHEKVNIIPL.IAKADTLTP.ECQQF
Retrocopy *DYLNAESQVNRHQMPDNRVKCCLYFVAPLGHRLKPLDIEFMKRLHEKVNIIPL<IAKADTLTPKECQQF

Parental  KKQIMKEIQEHKIKIYEFPETDDEEENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENG
          KKQIMKEI.E.KI..YEFPE.DDEEENK.VKK.KD.LPLAVVGSN.II.VNGKRVRGRQYPWG.AE.E.G
Retrocopy KKQIMKEIGENKI--YEFPESDDEEENKQVKKKKDHLPLAVVGSNIIIKVNGKRVRGRQYPWGMAEIEYG

Parental  EHCDFTILRNMLIRTHMQDLKDVT-NNVHYENYRSRKLAAVT
          .HCDFTILRNMLI.THMQDLKDVT..NVH.ENYRSRKLAAVT
Retrocopy KHCDFTILRNMLIITHMQDLKDVT>SNVHHENYRSRKLAAVT

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_1736 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1736 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 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012276	2 retrocopies	retro_cjac_1259, retro_cjac_3809,
Echinops telfairi	ENSETEG00000015624	3 retrocopies	retro_etel_1263, retro_etel_282, retro_etel_517,
Homo sapiens	ENSG00000122545	2 retrocopies	retro_hsap_3810, retro_hsap_4202,
Gorilla gorilla	ENSGGOG00000001175	1 retrocopy	retro_ggor_2816,
Monodelphis domestica	ENSMODG00000021167	1 retrocopy	retro_mdom_1672,
Nomascus leucogenys	ENSNLEG00000001673	1 retrocopy	retro_nleu_2152,
Otolemur garnettii	ENSOGAG00000006015	1 retrocopy	retro_ogar_1193,
Pongo abelii	ENSPPYG00000017639	1 retrocopy	retro_pabe_3438,
Pan troglodytes	ENSPTRG00000019080	2 retrocopies	retro_ptro_2585, retro_ptro_2853,
Rattus norvegicus	ENSRNOG00000006545	9 retrocopies	retro_rnor_1424, retro_rnor_1425, retro_rnor_1426, retro_rnor_1427, retro_rnor_1428, retro_rnor_1431, retro_rnor_1445, retro_rnor_1446, retro_rnor_821,
Sarcophilus harrisii	ENSSHAG00000003788	1 retrocopy	retro_shar_258,
Ictidomys tridecemlineatus	ENSSTOG00000013357	1 retrocopy	retro_itri_1227,
Ictidomys tridecemlineatus	ENSSTOG00000021378	3 retrocopies	retro_itri_1332, retro_itri_1736 , retro_itri_1771,
Ictidomys tridecemlineatus	ENSSTOG00000027666	1 retrocopy	retro_itri_2,