RetrogeneDB ID: retro_itri_740

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393316.1:1343981..1344732(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NECAP1
• Ensembl ID: ENSSTOG00000010153
• Aliases: None
• Description: NECAP endocytosis associated 1 [Source:HGNC Symbol;Acc:24539]

Sequence

>retro_itri_740
CCGGGGGGTTCCAACCACAGTAACAGGACATCTGACTGGAAATCAGAGCTGCCTGATTGGACTGGTTGTCTCCAAATCAC
TCCAAAAGGGAAGATTGCCTATATCAAACTCAAAAATAAAGTTTCGGGAGAGCTATTTGCCCAGGTACAGTAGAGCAATA
TCCTGGTATTGCTATGGAAACAGTGACAGATACTAGCTGCTACTTTGTAATTCGGATACAGGAATGGTACTAGGTGAAGT
GTGTTCATTGGCACTGGATTGACAGATCCGGGAGATGCCTTTGATGTTAATGTCTCCTTACAAGATCACTTCAAGTAGAT
AAAGCAGGAATCTTGAGATTTCTAAAGAATCTCAAGAAACGGACACTCGTCCCAAGTTGGCTTTAGGTTTCAAGGATGGA
CAGACCACCAAATTGAGTATCAGGAACATTACAATCAAGAAAGGAGGTGGTTTTAAGCCCAGGACTGCAGGAGCTGGGGG
TCTAAGCTTACTTTCTCCTCCTCCTGGAGGCAAAGTCACTATTCCGCCACCATCTTCTTCAGTTGCCATCGGTAATCATG
TCACCCCACCACCCATTCCAAAATCCAACCATGAAGGTATAATTCAGATGTTCTCATGGATTTGGATTCTCCTGCACCTG
TCACAACATCAGCTTCAGTTTTGGCAAGCAACGGATTGTGGGGAGATTTTAGTACTGCATCCAGCTCTGTTCCAAACCCA
GGCACCACAGCCACCCAACTGGGTCCAGTTT

Alignment

ORF - retro_itri_740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.43 %
• Parental protein coverage: 91.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PRASNRGYRASDWKLDQPDWTGRLRITSKGKIAYIKLEDKVSGELFAQAP-VEQYPGIAVETVTDSSRYF
          P..SN...R.SDWK...PDWTG.L.IT.KGKIAYIKL..KVSGELFAQ...VEQYPGIA.ETVTD.S.YF
Retrocopy PGGSNHSNRTSDWKSELPDWTGCLQITPKGKIAYIKLKNKVSGELFAQVQ<VEQYPGIAMETVTDTSCYF

Parental  VIRIQD-GTGRSAFIGIGFTDRGDAFDFNVSLQDHFKWVKQES-EISKESQEMDTRPKLDLGFKEGQTIK
          VIRIQ..GT..S.FIG.G.TD.GDAFD.NVSLQDHFK..KQES.EISKESQE.DTRPKL.LGFK.GQT.K
Retrocopy VIRIQE>GTR*SVFIGTGLTDPGDAFDVNVSLQDHFK*IKQES>EISKESQETDTRPKLALGFKDGQTTK

Parental  LSIGNITTKKGAASKPRTTGAGGLSLLPPPPGGKVTIPPPSSSVAISNHVTPPPIPKSNHGG-SNSDILL
          LSI.NIT.KKG...KPRT.GAGGLSLL.PPPGGKVTIPPPSSSVAI.NHVTPPPIPKSNH.G..NSD.L.
Retrocopy LSIRNITIKKGGGFKPRTAGAGGLSLLSPPPGGKVTIPPPSSSVAIGNHVTPPPIPKSNHEG<YNSDVLM

Parental  DLDSPVPVTTTAPAPVSASNDLWGDFSTASSSVPN-QAPQPSNWVQF
          DLDSP.PVTT...A.V.ASN.LWGDFSTASSSVPN.QAPQP.NWVQF
Retrocopy DLDSPAPVTTS--ASVLASNGLWGDFSTASSSVPN>QAPQPPNWVQF

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_740 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_740 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016989	1 retrocopy	retro_amel_1016,
Canis familiaris	ENSCAFG00000013930	1 retrocopy	retro_cfam_780,
Choloepus hoffmanni	ENSCHOG00000008087	3 retrocopies	retro_chof_1692, retro_chof_1818, retro_chof_1913,
Dasypus novemcinctus	ENSDNOG00000014778	2 retrocopies	retro_dnov_613, retro_dnov_986,
Homo sapiens	ENSG00000089818	1 retrocopy	retro_hsap_3839,
Gorilla gorilla	ENSGGOG00000010233	1 retrocopy	retro_ggor_2585,
Loxodonta africana	ENSLAFG00000002979	1 retrocopy	retro_lafr_632,
Mustela putorius furo	ENSMPUG00000016742	1 retrocopy	retro_mputfur_361,
Nomascus leucogenys	ENSNLEG00000001743	1 retrocopy	retro_nleu_1974,
Otolemur garnettii	ENSOGAG00000006358	1 retrocopy	retro_ogar_3442,
Pongo abelii	ENSPPYG00000004238	1 retrocopy	retro_pabe_3059,
Pan troglodytes	ENSPTRG00000023277	1 retrocopy	retro_ptro_2615,
Rattus norvegicus	ENSRNOG00000009236	1 retrocopy	retro_rnor_1806,
Ictidomys tridecemlineatus	ENSSTOG00000010153	2 retrocopies	retro_itri_1107, retro_itri_740 ,
Tursiops truncatus	ENSTTRG00000014260	1 retrocopy	retro_ttru_1035,