RetrogeneDB ID:

retro_nleu_1171

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397283.1:13215000..13215476(-)
Located in intron of:ENSNLEG00000012994
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SKP1
Ensembl ID:ENSNLEG00000008051
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1171
ATGCCGTCAATTAAGGTGCTGAGTTCTGATGGGGAGATATTCAATATGGAAATTGCCAAACAATCTGTGACTATCAAGAC
CATGTTGGAAGATTTGAGAACGGATGGAGATAATGACCCAGCTCCTCTACCAAAGTTAATGCAGCGATATTTTTAAAAGG
TCATTTGGTGGTGTACCCACCACAAAAATGGCCCTCCTCCTCCTGAGGATGATGCGAACAAAGAAAACGAACAGAGGAGA
TCCCTCCTTAGGACCAACAATTCCTGAAAGTCGATCAAGGAATACTTTTTCTACTTCTTCTGCCTGCAAACTACTTAGAC
ATCAAAGGTTTGCTTGATGTTACATGCAAGACTGTTGCCAATATGATCAAGGAGAAAAGTCCTGAGAAGATTCGCAAGAC
TTCCAATACCAAAAATGACTTTACTGAAGAAGAGGAAACCCAGGTACGCCAAGAGAACCAGCGGTGTGAACAGAAG

ORF - retro_nleu_1171 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.78 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPP
MPSIK..SSDGEIF....EIAKQSVTIKTMLEDL..D..GD.DP.PLP........KVI.WCTHHK..PP
RetrocopyMPSIKVLSSDGEIF--NMEIAKQSVTIKTMLEDLRTD--GDNDPAPLPKLMQRYF*KVIWWCTHHKNGPP
ParentalPPEDDENKE-KRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTF
PPEDD.NKE.KRT..IP..DQ.FLKVDQG.LF.L.L.ANYLDIKGLLDVTCKTVANMIK.K.PE.IRKT.
RetrocopyPPEDDANKE<KRTEEIPP*DQQFLKVDQGILFLLLLPANYLDIKGLLDVTCKTVANMIKEKSPEKIRKTS
ParentalNIKNDFTEEEEAQVRKENQWCEEK
N.KNDFTEEEE.QVR.ENQ.CE.K
RetrocopyNTKNDFTEEEETQVRQENQRCEQK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Nomascus leucogenys was not studied using ChIP-Seq data.

EST - click to see more details

Nomascus leucogenys was not studied using EST data.

TSS - click to see more details

Nomascus leucogenys was not studied using FANTOM5 data.

Lab - click to see more details

retro_nleu_1171 was not experimentally validated.

Retrocopy orthology:
Nomascus leucogenys 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.
Parental genes homology:
Parental genes homology involve 20 parental genes, and 120 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000009945 retrocopies
retro_cfam_1613, retro_cfam_779, retro_cfam_813, retro_cfam_889, retro_cfam_965,
Callithrix jacchus ENSCJAG000000136131 retrocopy
retro_cjac_112,
Cavia porcellus ENSCPOG000000051648 retrocopies
retro_cpor_1038, retro_cpor_1133, retro_cpor_1345, retro_cpor_1446, retro_cpor_223, retro_cpor_243, retro_cpor_830, retro_cpor_832,
Dipodomys ordii ENSDORG000000029123 retrocopies
retro_dord_338, retro_dord_512, retro_dord_720,
Equus caballus ENSECAG000000039312 retrocopies
retro_ecab_466, retro_ecab_789,
Echinops telfairi ENSETEG000000075605 retrocopies
retro_etel_1730, retro_etel_515, retro_etel_758, retro_etel_762, retro_etel_811,
Gorilla gorilla ENSGGOG000000229307 retrocopies
retro_ggor_1288, retro_ggor_1300, retro_ggor_2601, retro_ggor_2602, retro_ggor_2796, retro_ggor_2797, retro_ggor_778,
Microcebus murinus ENSMICG000000175883 retrocopies
retro_mmur_270, retro_mmur_803, retro_mmur_997,
Myotis lucifugus ENSMLUG0000002291913 retrocopies
retro_mluc_1455, retro_mluc_1738, retro_mluc_1895, retro_mluc_2009, retro_mluc_2260, retro_mluc_2261, retro_mluc_2520, retro_mluc_2527, retro_mluc_2557, retro_mluc_267, retro_mluc_383, retro_mluc_841, retro_mluc_944,
Macaca mulatta ENSMMUG000000130467 retrocopies
retro_mmul_1171, retro_mmul_2082, retro_mmul_2091, retro_mmul_2508, retro_mmul_654, retro_mmul_795, retro_mmul_919,
Monodelphis domestica ENSMODG000000141684 retrocopies
retro_mdom_1173, retro_mdom_155, retro_mdom_1648, retro_mdom_929,
Mus musculus ENSMUSG000000363091 retrocopy
retro_mmus_2518,
Nomascus leucogenys ENSNLEG00000008051 7 retrocopies
retro_nleu_1171 , retro_nleu_1615, retro_nleu_1667, retro_nleu_2290, retro_nleu_323, retro_nleu_472, retro_nleu_827,
Ochotona princeps ENSOPRG000000066377 retrocopies
retro_opri_1199, retro_opri_188, retro_opri_23, retro_opri_513, retro_opri_547, retro_opri_902, retro_opri_955,
Pongo abelii ENSPPYG000000157837 retrocopies
retro_pabe_1915, retro_pabe_199, retro_pabe_2072, retro_pabe_2736, retro_pabe_2756, retro_pabe_626, retro_pabe_824,
Pteropus vampyrus ENSPVAG000000124274 retrocopies
retro_pvam_1040, retro_pvam_1137, retro_pvam_1269, retro_pvam_503,
Sorex araneus ENSSARG000000083074 retrocopies
retro_sara_241, retro_sara_446, retro_sara_492, retro_sara_609,
Tupaia belangeri ENSTBEG0000001554415 retrocopies
retro_tbel_1227, retro_tbel_1279, retro_tbel_1327, retro_tbel_1758, retro_tbel_1787, retro_tbel_1903, retro_tbel_1905, retro_tbel_240, retro_tbel_3024, retro_tbel_3267, retro_tbel_3848, retro_tbel_405, retro_tbel_4095, retro_tbel_528, retro_tbel_711,
Tarsius syrichta ENSTSYG0000001069611 retrocopies
retro_tsyr_1037, retro_tsyr_1370, retro_tsyr_1400, retro_tsyr_1896, retro_tsyr_1924, retro_tsyr_2058, retro_tsyr_210, retro_tsyr_336, retro_tsyr_396, retro_tsyr_464, retro_tsyr_762,
Tursiops truncatus ENSTTRG000000168586 retrocopies
retro_ttru_1344, retro_ttru_1764, retro_ttru_1801, retro_ttru_656, retro_ttru_657, retro_ttru_961,


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