RetrogeneDB ID:

retro_pabe_599

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:10:65159172..65159604(-)
Located in intron of:ENSPPYG00000002374
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CALM1
Ensembl ID:ENSPPYG00000012430
Aliases:None
Description:calmodulin [Source:RefSeq peptide;Acc:NP_001126243]


Retrocopy-Parental alignment summary:






>retro_pabe_599
ATGGCTGACCAACTGACTGAAGAGCAGATTGCAGAATTCAAAGTTTTGTCACCATTTGACAAAGATGGTGATGGAACTAT
AACAACAAAGAAACTGGGAATTGTAATGAGGTCTTAGGCAGAATCCCACAGAAGCAGAGTTACAGGACATGATTAATGAA
GTAAATGCTGATGGTAATGGCACAATTGACTTCCCTGAACTTCTGACAATGATGGCAAAAAAAATGAAAGACACAGTGAA
GAAGAAATTAGAGAAGCATTCTGTGTGTTTGATAAGGATGGCAATGGCTATATTAGTGGTGTAGAACTTCACCATGTGAT
GACAAACCTTGGAGTGAAGTTAACAGACGAAGAAGTTGATTAAATGATCAGGGAAGCAGATCCTGATGGTGATGGTCAAG
TAAACTATGAGTTTGTACAAATGATGACAGCA

ORF - retro_pabe_599 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.78 %
Parental protein coverage: 99.33 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRS-LG-QNPTEAELQDMINEVDADGNGTIDFPE
MADQLTEEQIAEFK...S.FDKDGDGTITTK.LG.VMRS.LG.QNPTEAELQDMINEV.ADGNGTIDFPE
RetrocopyMADQLTEEQIAEFK-VLSPFDKDGDGTITTKKLGIVMRS<LG<QNPTEAELQDMINEVNADGNGTIDFPE
ParentalFLTMMARKMKDT-DSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQV
.LTMM....KDT...EE.IREAF.VFDKDGNGYIS..EL.HVMTNLG.KLTDEEVD.MIREAD.DGDGQV
RetrocopyLLTMMXXXXKDT<SEEE-IREAFCVFDKDGNGYISGVELHHVMTNLGVKLTDEEVD*MIREADPDGDGQV
ParentalNYEEFVQMMTA
NY.EFVQMMTA
RetrocopyNY-EFVQMMTA

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .33 RPM 591 .44 RPM
SRP007412_cerebellum 1 .58 RPM 604 .11 RPM
SRP007412_heart 0 .33 RPM 141 .85 RPM
SRP007412_kidney 0 .30 RPM 180 .72 RPM
SRP007412_liver 0 .70 RPM 153 .53 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_599 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_599 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_599 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_522
Callithrix jacchus retro_cjac_1039
Parental genes homology:
Parental genes homology involve 35 parental genes, and 131 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000157121 retrocopy
retro_acar_45,
Ailuropoda melanoleuca ENSAMEG000000062042 retrocopies
retro_amel_63, retro_amel_72,
Choloepus hoffmanni ENSCHOG000000082456 retrocopies
retro_chof_1940, retro_chof_2261, retro_chof_367, retro_chof_735, retro_chof_833, retro_chof_965,
Callithrix jacchus ENSCJAG000000006384 retrocopies
retro_cjac_1039, retro_cjac_1401, retro_cjac_2859, retro_cjac_4097,
Cavia porcellus ENSCPOG000000121813 retrocopies
retro_cpor_1012, retro_cpor_87, retro_cpor_89,
Equus caballus ENSECAG000000083964 retrocopies
retro_ecab_15, retro_ecab_59, retro_ecab_750, retro_ecab_882,
Erinaceus europaeus ENSEEUG000000000403 retrocopies
retro_eeur_38, retro_eeur_561, retro_eeur_671,
Echinops telfairi ENSETEG000000093775 retrocopies
retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Echinops telfairi ENSETEG0000001866716 retrocopies
retro_etel_1032, retro_etel_1075, retro_etel_108, retro_etel_1164, retro_etel_1184, retro_etel_1507, retro_etel_1650, retro_etel_1683, retro_etel_1903, retro_etel_2139, retro_etel_22, retro_etel_539, retro_etel_687, retro_etel_864, retro_etel_902, retro_etel_951,
Ficedula albicollis ENSFALG000000128281 retrocopy
retro_falb_16,
Felis catus ENSFCAG000000291415 retrocopies
retro_fcat_1926, retro_fcat_591, retro_fcat_629, retro_fcat_87, retro_fcat_88,
Gadus morhua ENSGMOG000000093421 retrocopy
retro_gmor_23,
Latimeria chalumnae ENSLACG000000050591 retrocopy
retro_lcha_53,
Loxodonta africana ENSLAFG000000098651 retrocopy
retro_lafr_655,
Myotis lucifugus ENSMLUG000000290166 retrocopies
retro_mluc_13, retro_mluc_1732, retro_mluc_18, retro_mluc_19, retro_mluc_2207, retro_mluc_2258,
Macaca mulatta ENSMMUG000000174661 retrocopy
retro_mmul_256,
Monodelphis domestica ENSMODG000000092221 retrocopy
retro_mdom_1126,
Mustela putorius furoENSMPUG000000120614 retrocopies
retro_mputfur_1207, retro_mputfur_21, retro_mputfur_838, retro_mputfur_942,
Oryctolagus cuniculus ENSOCUG000000021072 retrocopies
retro_ocun_1468, retro_ocun_84,
Otolemur garnettii ENSOGAG000000088246 retrocopies
retro_ogar_1126, retro_ogar_1196, retro_ogar_1432, retro_ogar_1535, retro_ogar_209, retro_ogar_2326,
Ochotona princeps ENSOPRG000000154787 retrocopies
retro_opri_1129, retro_opri_1155, retro_opri_16, retro_opri_40, retro_opri_506, retro_opri_830, retro_opri_86,
Petromyzon marinus ENSPMAG000000033231 retrocopy
retro_pmar_12,
Pongo abelii ENSPPYG000000060601 retrocopy
retro_pabe_1045,
Pongo abelii ENSPPYG000000101544 retrocopies
retro_pabe_1106, retro_pabe_1466, retro_pabe_3238, retro_pabe_3676,
Pongo abelii ENSPPYG00000012430 5 retrocopies
retro_pabe_1068, retro_pabe_1133, retro_pabe_115, retro_pabe_45, retro_pabe_599 ,
Pelodiscus sinensis ENSPSIG000000131731 retrocopy
retro_psin_9,
Pan troglodytes ENSPTRG000000119014 retrocopies
retro_ptro_1195, retro_ptro_2623, retro_ptro_83, retro_ptro_881,
Pteropus vampyrus ENSPVAG000000051832 retrocopies
retro_pvam_558, retro_pvam_560,
Sorex araneus ENSSARG000000087311 retrocopy
retro_sara_119,
Sus scrofa ENSSSCG000000084331 retrocopy
retro_sscr_228,
Ictidomys tridecemlineatus ENSSTOG000000218147 retrocopies
retro_itri_1048, retro_itri_1473, retro_itri_37, retro_itri_433, retro_itri_68, retro_itri_778, retro_itri_859,
Tupaia belangeri ENSTBEG0000000056917 retrocopies
retro_tbel_1450, retro_tbel_24, retro_tbel_2418, retro_tbel_258, retro_tbel_2612, retro_tbel_2856, retro_tbel_2933, retro_tbel_3150, retro_tbel_3195, retro_tbel_3956, retro_tbel_4141, retro_tbel_4171, retro_tbel_4212, retro_tbel_4324, retro_tbel_675, retro_tbel_722, retro_tbel_765,
Taeniopygia guttata ENSTGUG000000025811 retrocopy
retro_tgut_6,
Tarsius syrichta ENSTSYG000000125645 retrocopies
retro_tsyr_1641, retro_tsyr_2012, retro_tsyr_2128, retro_tsyr_2148, retro_tsyr_576,
Vicugna pacos ENSVPAG000000092861 retrocopy
retro_vpac_442,


Copyright © RetrogeneDB 2014-2017