RetrogeneDB ID:

retro_pabe_2995

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:6:118412973..118413305(-)
Located in intron of:ENSPPYG00000016943
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NIP7
Ensembl ID:ENSPPYG00000007503
Aliases:None
Description:60S ribosome subunit biogenesis protein NIP7 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5R9J1]


Retrocopy-Parental alignment summary:






>retro_pabe_2995
GGGACCTGCTTCAGAAAATTCACCAAGACCTACAAGTTTCAGTTGAACATCACAGCTCTGGATTACCCTGCACCCTATGC
CAAGTATAAAGTGTGGATAAAACCTGGAGCACAGCAGTCCTTCCTATATGGGGACGATATGTTGAAATCTGGTCTGAATC
AAATCACGAAAAATACTTCTCCTGGCCAGGAAGTGGTGGTGGCAGACATCCCTTTGGGTTTTGGGGTGGCAGCCACATCT
ACGCAAGACTGCAGAAAAGGAGACCCCACCGATTTGTGGTATTTCATCAAGCAAACACTGACGAATATGTGCAGCACGAA
GAGACGGTGACT

ORF - retro_pabe_2995 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.91 %
Parental protein coverage: 63.33 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGTCFGKFTKTHKFRLHVTALDYLAPYAKYKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSM
GTCF.KFTKT.KF.L..TALDY.APYAKYKVWIKPGA.QSFLYG...LKSGL..IT.NTS..Q.VVV...
RetrocopyGTCFRKFTKTYKFQLNITALDYPAPYAKYKVWIKPGAQQSFLYGDDMLKSGLNQITKNTSPGQEVVV---
ParentalADIPLGFGVAAKSTQDCRKVDPMAI-VVFHQADIGEYVRHEETLT
ADIPLGFGVAA.STQDCRK.DP....VVFHQA...EYV.HEET.T
RetrocopyADIPLGFGVAATSTQDCRKGDPTDL<VVFHQANTDEYVQHEETVT

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 .00 RPM 10 .95 RPM
SRP007412_cerebellum 0 .00 RPM 6 .93 RPM
SRP007412_heart 0 .00 RPM 4 .52 RPM
SRP007412_kidney 0 .00 RPM 11 .37 RPM
SRP007412_liver 0 .00 RPM 10 .68 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_2995 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2995 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2995 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3648
Pan troglodytes retro_ptro_2473
Gorilla gorilla retro_ggor_2464
Macaca mulatta retro_mmul_1801
Callithrix jacchus retro_cjac_2466
Parental genes homology:
Parental genes homology involve 21 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000075421 retrocopy
retro_amel_938,
Bos taurus ENSBTAG000000016661 retrocopy
retro_btau_353,
Canis familiaris ENSCAFG000000298352 retrocopies
retro_cfam_1346, retro_cfam_1682,
Callithrix jacchus ENSCJAG000000153642 retrocopies
retro_cjac_2466, retro_cjac_4212,
Dasypus novemcinctus ENSDNOG000000068212 retrocopies
retro_dnov_2114, retro_dnov_74,
Homo sapiens ENSG000001326032 retrocopies
retro_hsap_2707, retro_hsap_3648,
Gorilla gorilla ENSGGOG000000227852 retrocopies
retro_ggor_1886, retro_ggor_2464,
Microcebus murinus ENSMICG000000096641 retrocopy
retro_mmur_5,
Myotis lucifugus ENSMLUG000000118353 retrocopies
retro_mluc_1119, retro_mluc_2171, retro_mluc_2508,
Macaca mulatta ENSMMUG000000166352 retrocopies
retro_mmul_1801, retro_mmul_192,
Monodelphis domestica ENSMODG000000027822 retrocopies
retro_mdom_1011, retro_mdom_1709,
Mus musculus ENSMUSG000000319172 retrocopies
retro_mmus_1858, retro_mmus_2281,
Nomascus leucogenys ENSNLEG000000054922 retrocopies
retro_nleu_1579, retro_nleu_510,
Oryctolagus cuniculus ENSOCUG000000176525 retrocopies
retro_ocun_1013, retro_ocun_1262, retro_ocun_1292, retro_ocun_491, retro_ocun_721,
Otolemur garnettii ENSOGAG000000080662 retrocopies
retro_ogar_1619, retro_ogar_2453,
Pongo abelii ENSPPYG00000007503 2 retrocopies
retro_pabe_2258, retro_pabe_2995 ,
Pan troglodytes ENSPTRG000000082792 retrocopies
retro_ptro_1828, retro_ptro_2473,
Rattus norvegicus ENSRNOG000000203918 retrocopies
retro_rnor_1279, retro_rnor_1566, retro_rnor_1567, retro_rnor_1674, retro_rnor_1676, retro_rnor_485, retro_rnor_655, retro_rnor_865,
Sorex araneus ENSSARG000000003031 retrocopy
retro_sara_665,
Ictidomys tridecemlineatus ENSSTOG000000128711 retrocopy
retro_itri_1368,
Tursiops truncatus ENSTTRG000000100122 retrocopies
retro_ttru_1783, retro_ttru_676,




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