RetrogeneDB ID: retro_itri_1163

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393390.1:6119099..6119963(-)
• Located in intron of: ENSSTOG00000010592

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA1191
• Ensembl ID: ENSSTOG00000000946
• Aliases: None
• Description: KIAA1191 [Source:HGNC Symbol;Acc:29209]

Sequence

>retro_itri_1163
CCCCTAGGCAAGATGTCCCTGCCCATCGGGATGTGCCCGTCGGGCATTCAGCTATGATGATGCCCTTGAGGACCCTGCAC
CCTTGACTCCTCCTCCATCGGACATGGGCAGCATCCCCTGGAAGCCAGTGATTCCAGAGGGCAAGTATCAGCACCTTGCC
GAGGAGGAAGGAGAGGCCAATGTATCCCCCCCTGCCATGACCCTGTCAACAGTCACTGACAGTACCGACAAGGTCCTGAT
GGTAAAGGCCAAAGCTACCCATGTCGTCATGAATTTTCTGATTACAAAACAGACACAGGAGAGCATTCAGCATTTTGAAC
AACAGGCAGGACCTAGAGATTCTGGCTACACACCCCACAAAGGCCTTACCTCCGAGGAAACCAAGTACCTCTGACTAGCA
GAAGCACTCCACAAGCTAAAGCTGCAGAGTGGAGAGAGGACAAAGGAAGAGAAGCAGCCTGCATCGCCCAGTCACCCCAA
GCAGCAGCCCTCACTCTTCCCTTAAGCAGAGGCCGGAGGCTGGTTTTCTTCTGGTTCCTCTTAGCCTTACCTGGCCCAAG
TCCTAGCACCATGGATCCTGGAAGTGGAGATAAGGACAGAAACTCATCAGATAAATGGAGCCTTTTTGGTCCAAGACCCC
TTCAGAAGTCCGATTCTGGAGCTTTTGCCATCCAGGCCTACAAAGACGCCCAGAAGCCCTCTCCCATGGAGCTGATCCAT
GCCCAGGCCACCCGAATGGCTGGAGATCCGGCAACCTTCAAGCCACCCAAAGTGGATGTCCCAGTCATAGAAGGGAAGAA
ACCACTGCCTCGGACCCATAATCTCAAACCTCGTGACTTGAATGTGCTCACACCCACTGGCTTT

Alignment

ORF - retro_itri_1163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.49 %
• Parental protein coverage: 95.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PLGKMSLPIGMC-RRAFSYDDALEDPAPMTPPPSDMGSIPWKPVIPERKYQHLAKEEEGEASVSHPAMTL
          PLGKMSLPIGMC.RRAFSYDDALEDPAP.TPPPSDMGSIPWKPVIPE.KYQHLA.EEEGEA.VS.PAMTL
Retrocopy PLGKMSLPIGMC>RRAFSYDDALEDPAPLTPPPSDMGSIPWKPVIPEGKYQHLA-EEEGEANVSPPAMTL

Parental  STVTDSTDKVPVVKAKATHVIMNSLITKQTQESIQRFEQQAGLRDAGYTPHKGLTTEETKYLRVAEALHK
          STVTDSTDKV..VKAKATHV.MN.LITKQTQESIQ.FEQQAG.RD.GYTPHKGLT.EETKYL..AEALHK
Retrocopy STVTDSTDKVLMVKAKATHVVMNFLITKQTQESIQHFEQQAGPRDSGYTPHKGLTSEETKYL*LAEALHK

Parental  LKLQSGEITKEEKQPAS-AQS-TPSSSPHSSPKQRPR-GWFSSGSS-VALPGPSPSTMDPGSGDKDRNSS
          LKLQSGE.TKEEKQPAS.AQS.TPSSSPHSS.KQRP..GWFSSGSS..ALPGPSPSTMDPGSGDKDRNSS
Retrocopy LKLQSGERTKEEKQPAS<AQS<TPSSSPHSSLKQRPE<GWFSSGSS<LALPGPSPSTMDPGSGDKDRNSS

Parental  DKWSLFGPRPLQKSDSG-FTIQAYKGAQKPSPMELIRAQATRMAEDPATFKPPKMDIPVIEGKKPLPRTH
          DKWSLFGPRPLQKSDSG.F.IQAYK.AQKPSPMELI.AQATRMA.DPATFKPPK.D.PVIEGKKPLPRTH
Retrocopy DKWSLFGPRPLQKSDSGAFAIQAYKDAQKPSPMELIHAQATRMAGDPATFKPPKVDVPVIEGKKPLPRTH

Parental  NLKPRDLNVLTPTGF
          NLKPRDLNVLTPTGF
Retrocopy NLKPRDLNVLTPTGF

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_1163 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1163 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 25 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006123	4 retrocopies	retro_chof_1411, retro_chof_1751, retro_chof_2197, retro_chof_959,
Callithrix jacchus	ENSCJAG00000012337	2 retrocopies	retro_cjac_1699, retro_cjac_901,
Cavia porcellus	ENSCPOG00000019402	1 retrocopy	retro_cpor_625,
Dasypus novemcinctus	ENSDNOG00000002676	3 retrocopies	retro_dnov_2220, retro_dnov_753, retro_dnov_976,
Equus caballus	ENSECAG00000003238	1 retrocopy	retro_ecab_621,
Felis catus	ENSFCAG00000007189	1 retrocopy	retro_fcat_1625,
Homo sapiens	ENSG00000122203	4 retrocopies	retro_hsap_1641, retro_hsap_3089, retro_hsap_524, retro_hsap_817,
Gorilla gorilla	ENSGGOG00000023834	4 retrocopies	retro_ggor_1240, retro_ggor_2122, retro_ggor_482, retro_ggor_669,
Loxodonta africana	ENSLAFG00000028878	1 retrocopy	retro_lafr_313,
Myotis lucifugus	ENSMLUG00000003498	1 retrocopy	retro_mluc_667,
Macaca mulatta	ENSMMUG00000003921	3 retrocopies	retro_mmul_1082, retro_mmul_1566, retro_mmul_1971,
Monodelphis domestica	ENSMODG00000005274	6 retrocopies	retro_mdom_116, retro_mdom_1992, retro_mdom_218, retro_mdom_56, retro_mdom_722, retro_mdom_751,
Mustela putorius furo	ENSMPUG00000012579	1 retrocopy	retro_mputfur_1237,
Mus musculus	ENSMUSG00000025871	2 retrocopies	retro_mmus_1580, retro_mmus_737,
Nomascus leucogenys	ENSNLEG00000012473	4 retrocopies	retro_nleu_1327, retro_nleu_2233, retro_nleu_251, retro_nleu_2578,
Oryctolagus cuniculus	ENSOCUG00000012191	3 retrocopies	retro_ocun_1263, retro_ocun_1415, retro_ocun_1509,
Otolemur garnettii	ENSOGAG00000008281	6 retrocopies	retro_ogar_1543, retro_ogar_1986, retro_ogar_2289, retro_ogar_3002, retro_ogar_3075, retro_ogar_781,
Procavia capensis	ENSPCAG00000008839	1 retrocopy	retro_pcap_277,
Pongo abelii	ENSPPYG00000016068	4 retrocopies	retro_pabe_223, retro_pabe_2558, retro_pabe_2615, retro_pabe_729,
Pan troglodytes	ENSPTRG00000017558	5 retrocopies	retro_ptro_1111, retro_ptro_2086, retro_ptro_2975, retro_ptro_392, retro_ptro_568,
Pteropus vampyrus	ENSPVAG00000012448	1 retrocopy	retro_pvam_118,
Rattus norvegicus	ENSRNOG00000017133	2 retrocopies	retro_rnor_968, retro_rnor_969,
Ictidomys tridecemlineatus	ENSSTOG00000000946	2 retrocopies	retro_itri_1163 , retro_itri_960,
Tupaia belangeri	ENSTBEG00000013189	1 retrocopy	retro_tbel_2271,
Tursiops truncatus	ENSTTRG00000005376	1 retrocopy	retro_ttru_383,