RetrogeneDB ID:

retro_pabe_3358

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:8:108064447..108064964(-)
Located in intron of:ENSPPYG00000018794
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SARNP
Ensembl ID:ENSPPYG00000004630
Aliases:SARNP, CIP29, HCC1
Description:SAP domain-containing ribonucleoprotein [Source:UniProtKB/Swiss-Prot;Acc:Q5R4V4]


Retrocopy-Parental alignment summary:






>retro_pabe_3358
CTCCAGGCATATCTTTCAGGGCATGCTGAAGAGGCAAATGAAGAAGTACTGGGAGATGAAACAGAGAAAGAAGAAACAAA
GCCCCATAGAAATCCCTGTCAAAGAGGAAGAACTCCCTGAAAAAACTGTTGATGTGGAAGCAGAGAAGAAAGTGGTAAAA
ATTACATCTGAAATACCACAGGCGGAGAGAACGCAGAAGAGGGCTGAACGAGTCCATGTACCTGTGAGCCTGTAAAGTAA
GAAAACTGCCCAGGCAGCTAGGTTTGGGACTTCTTCAGTTTCAACAAAAGGTCTGCCATCTAACAACAAACCTATCATGA
ACCTGGATAAGCTAAAGGAAAGAGCTCAAAGATTTGGTTTGAATGGCTCTTCAATCTCCATAAAGTCTGAAGATGGTGAG
AAACTGAAAAGGAGGAAGGAGCGATTTGGAATTATCACCGGTTCAGCTGGAACCGGAAGGAACACAGAGGATACAGAGGC
AAAGAATAGGAAAAGAGCCGCATGCTGTGGGATTGCC

ORF - retro_pabe_3358 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.57 %
Parental protein coverage: 82.38 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalLQAYLEEHAEEEANEEDVLGDETEEEETKP-IELPVKEEEPPEKTVDVAAEKKVVKITSEIPQTERMQKR
LQAYL..HAEE.ANEE.VLGDETE.EETKP.IE.PVKEEE.PEKTVDV.AEKKVVKITSEIPQ.ER.QKR
RetrocopyLQAYLSGHAEE-ANEE-VLGDETEKEETKP>IEIPVKEEELPEKTVDVEAEKKVVKITSEIPQAERTQKR
ParentalAERFNVPVSLESKKAARAARFGISSVPTKGLSSDNKPMVNLDKLKERAQRFGLNVSSISRKSEDDEKLKK
AER..VPVSL.SKK.A.AARFG.SSV.TKGL.S.NKP..NLDKLKERAQRFGLN.SSIS.KSED.EKLK.
RetrocopyAERVHVPVSL*SKKTAQAARFGTSSVSTKGLPSNNKPIMNLDKLKERAQRFGLNGSSISIKSEDGEKLKR
ParentalRKERFGIVTSSAGTG-TTEDTEAKKRKRAERFGIA
RKERFGI.T.SAGTG..TEDTEAK.RKRA...GIA
RetrocopyRKERFGIITGSAGTGRNTEDTEAKNRKRAACCGIA

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 18 .63 RPM
SRP007412_cerebellum 0 .00 RPM 21 .04 RPM
SRP007412_heart 0 .00 RPM 16 .74 RPM
SRP007412_kidney 0 .00 RPM 19 .23 RPM
SRP007412_liver 0 .00 RPM 11 .17 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_3358 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3358 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3358 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2782
Callithrix jacchus retro_cjac_1487
Parental genes homology:
Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000117692 retrocopies
retro_amel_1602, retro_amel_347,
Bos taurus ENSBTAG000000206621 retrocopy
retro_btau_202,
Callithrix jacchus ENSCJAG000000078538 retrocopies
retro_cjac_1070, retro_cjac_1487, retro_cjac_1801, retro_cjac_2439, retro_cjac_2560, retro_cjac_389, retro_cjac_4139, retro_cjac_731,
Cavia porcellus ENSCPOG000000117551 retrocopy
retro_cpor_1313,
Dipodomys ordii ENSDORG000000010651 retrocopy
retro_dord_80,
Erinaceus europaeus ENSEEUG000000151761 retrocopy
retro_eeur_549,
Homo sapiens ENSG000002053231 retrocopy
retro_hsap_3882,
Gorilla gorilla ENSGGOG000000132172 retrocopies
retro_ggor_2613, retro_ggor_2753,
Loxodonta africana ENSLAFG000000150531 retrocopy
retro_lafr_1024,
Microcebus murinus ENSMICG000000109021 retrocopy
retro_mmur_358,
Monodelphis domestica ENSMODG000000289491 retrocopy
retro_mdom_1909,
Mustela putorius furoENSMPUG000000008851 retrocopy
retro_mputfur_617,
Mus musculus ENSMUSG000000784271 retrocopy
retro_mmus_54,
Nomascus leucogenys ENSNLEG000000175992 retrocopies
retro_nleu_2779, retro_nleu_569,
Procavia capensis ENSPCAG000000094772 retrocopies
retro_pcap_262, retro_pcap_45,
Pongo abelii ENSPPYG00000004630 2 retrocopies
retro_pabe_3116, retro_pabe_3358 ,
Pan troglodytes ENSPTRG000000297472 retrocopies
retro_ptro_2644, retro_ptro_2782,
Rattus norvegicus ENSRNOG000000305202 retrocopies
retro_rnor_1326, retro_rnor_471,


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