RetrogeneDB ID: retro_itri_1292

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393429.1:1404076..1404589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KATNBL1
• Ensembl ID: ENSSTOG00000003813
• Aliases: None
• Description: katanin p80 subunit B-like 1 [Source:HGNC Symbol;Acc:26199]

Sequence

>retro_itri_1292
AAAAAGATCTCTAATTTCACTAATAAAAACATGAAGCATGTTAAGAAATCTCTAAAACAGTTGGCTGCTTTTATAAATAC
AACAGTTGAATGCAACATCCTTCCCCAAATCCTTGTTATAGTAAAAGAACAGCTCTCTAGATAAATGGGAACTGCTACAT
GGCAAATAAAGAAAATGAACTGGCTTGTGCAGGCTACCTGCCTGCAAAATTATGCCATGATGATCATACATATTTGGTTA
ACTCCAGTGATTCTGGTTCTTCACAGACAGGAAAACTCATCATCTAAATACAGTGTTTTGGGTTTTTTTCCTGAGGTTTC
TCTGGATCATGAAACAATGGCCCAAGCTTTGTTTAGCAGGAGTTTGAGATTGAATGTAGCTTTAACTTTCTGGACAAAGA
GAAGTATAAGTGAACTTGTAGCTTATTTAGTAAGAACAAAAGATCTTAGAGTTGTGGTAGACTGCCTGCCTGTACTCACT
AATAATTCACATGAATAAAAATAATATCTCACT

Alignment

ORF - retro_itri_1292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.16 %
• Parental protein coverage: 55.26 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KQLAAYINRTVGQAVKSPDKLRKVIYRRKK-VQHPFPNPCYRKKQSP-ISGGCDMANKENELACAGHLPE
          K......N.......KS...L...I.......QHP.PNPCY.K.....I.G.C.MANKENELACAG.LP.
Retrocopy KKISNFTNKNMKHVKKSLKQLAAFINTTVE<MQHPSPNPCYSKRTAL*INGNCYMANKENELACAGYLPA

Parental  KLHHDSRTYLVNSSDSGTSQT-ESPSSKYS--GFFSEVSQDHETMAQVLFSRNLRLNVALTFWRKRSISE
          KL.HD..TYLVNSSDSG.SQT.E..SSKYS..GFF.EVS.DHETMAQ.LFSR.LRLNVALTFW.KRSISE
Retrocopy KLCHDDHTYLVNSSDSGSSQT>ENSSSKYSVLGFFPEVSLDHETMAQALFSRSLRLNVALTFWTKRSISE

Parental  LVAYLVRIEDLGVVVDCLPVLTNSLQEEKQYIS
          LVAYLVR..DL.VVVDCLPVLTN...E.K.Y..
Retrocopy LVAYLVRTKDLRVVVDCLPVLTNNSHE*K*YLT

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_1292 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1292 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 24 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006413	2 retrocopies	retro_btau_1198, retro_btau_1776,
Callithrix jacchus	ENSCJAG00000021110	3 retrocopies	retro_cjac_1971, retro_cjac_265, retro_cjac_2971,
Cavia porcellus	ENSCPOG00000011153	2 retrocopies	retro_cpor_1374, retro_cpor_1410,
Dasypus novemcinctus	ENSDNOG00000016279	5 retrocopies	retro_dnov_1586, retro_dnov_2201, retro_dnov_2253, retro_dnov_248, retro_dnov_957,
Dipodomys ordii	ENSDORG00000013172	2 retrocopies	retro_dord_378, retro_dord_730,
Equus caballus	ENSECAG00000023450	1 retrocopy	retro_ecab_841,
Echinops telfairi	ENSETEG00000001640	7 retrocopies	retro_etel_1169, retro_etel_1341, retro_etel_2032, retro_etel_2062, retro_etel_319, retro_etel_518, retro_etel_635,
Homo sapiens	ENSG00000134152	3 retrocopies	retro_hsap_3171, retro_hsap_3677, retro_hsap_425,
Gorilla gorilla	ENSGGOG00000014230	3 retrocopies	retro_ggor_1347, retro_ggor_2486, retro_ggor_415,
Macropus eugenii	ENSMEUG00000015610	4 retrocopies	retro_meug_1035, retro_meug_1899, retro_meug_1900, retro_meug_646,
Myotis lucifugus	ENSMLUG00000001532	2 retrocopies	retro_mluc_214, retro_mluc_633,
Macaca mulatta	ENSMMUG00000000013	1 retrocopy	retro_mmul_2005,
Mustela putorius furo	ENSMPUG00000008019	1 retrocopy	retro_mputfur_1258,
Nomascus leucogenys	ENSNLEG00000010772	2 retrocopies	retro_nleu_1020, retro_nleu_2679,
Oryctolagus cuniculus	ENSOCUG00000017654	5 retrocopies	retro_ocun_1065, retro_ocun_343, retro_ocun_614, retro_ocun_877, retro_ocun_975,
Otolemur garnettii	ENSOGAG00000015633	3 retrocopies	retro_ogar_1643, retro_ogar_2219, retro_ogar_3301,
Ochotona princeps	ENSOPRG00000010379	1 retrocopy	retro_opri_446,
Pongo abelii	ENSPPYG00000006309	2 retrocopies	retro_pabe_2634, retro_pabe_646,
Pan troglodytes	ENSPTRG00000006877	3 retrocopies	retro_ptro_2271, retro_ptro_2491, retro_ptro_323,
Sorex araneus	ENSSARG00000007891	1 retrocopy	retro_sara_345,
Ictidomys tridecemlineatus	ENSSTOG00000003813	1 retrocopy	retro_itri_1292 ,
Tupaia belangeri	ENSTBEG00000001614	7 retrocopies	retro_tbel_1267, retro_tbel_127, retro_tbel_1362, retro_tbel_2139, retro_tbel_3276, retro_tbel_4552, retro_tbel_984,
Tarsius syrichta	ENSTSYG00000011059	1 retrocopy	retro_tsyr_2135,
Vicugna pacos	ENSVPAG00000007170	1 retrocopy	retro_vpac_632,