RetrogeneDB ID:

retro_pabe_2735

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:56814437..56815107(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:AK4
Ensembl ID:ENSPPYG00000001269
Aliases:AK3, AK 4, AK3L1, AK4
Description:Adenylate kinase isoenzyme 4, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5R421]


Retrocopy-Parental alignment summary:






>retro_pabe_2735
GTGGCTTCCAAACTCCCGCGCGCAGTCATCCTCAGGCCCCCCTGCTCGGGCAAGGGCACAGTGTGCCAGAGGATCGCCCA
GAACTTTGGCTTCCAGGATCTCTCCAGCGGGCACTTCTTGCGGGAGAATATCAAGGCCAACACCGAAGTTGGTGAGATGG
CAAAACAGTATATAGAGAAAAGTCTTTTGGTTCCAGACCATGTGATCACACGCCTAATGATGTCTGAGTTGGAGAACAGC
CGTGGCCAGCACTGGCTCCTCGATGGTTTTCCTAGGACGTTACGACAAGCTGAAGCCCTGGACAAAAATCTGTGAAGTGG
ATTTAGTAATCAGTTTGAAAATTCCATTTGAAACACTTAAAGATCGTCTCAGCTGCTGTTGGATTCACCCTCCTAGGGGA
AGGGTATATAACATGGACTTCAATCCACCTCATATACATGGGATTGATGACGTCACTGGTGAACCATTAGTCCAGTAGGA
GGATGATAAACCTGAAGCAGCTGCTGCCAGGCTAAGACAGTACAAGTATATGGCAAAGCCAGTCGCTGAATTATACAAGA
GCCGAGGAGTTCTCCACCAATTTTCTGGGACAGAGACGAACAAAATCTGGCCCTATGTTTACACACTTTTCTCGAACATG
ATCACACCTATTCAGTCCAAAGAAGCATAT

ORF - retro_pabe_2735 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.62 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMASKLLRAVILGPPGSGKGTVCQRIAQNFGLQHLSSGHFLRENIKANTEVGEMAKQYIEKSLLVPDHVIT
.ASKL.RAVIL.PP.SGKGTVCQRIAQNFG.Q.LSSGHFLRENIKANTEVGEMAKQYIEKSLLVPDHVIT
RetrocopyVASKLPRAVILRPPCSGKGTVCQRIAQNFGFQDLSSGHFLRENIKANTEVGEMAKQYIEKSLLVPDHVIT
ParentalRLMMSELENRRGQHWLLDGFPRTLGQAEALDK-ICEVDLVISLNIPFETLKDRLSRRWIHPPSGRVYNLD
RLMMSELEN.RGQHWLLDGFPRTL.QAEALDK.ICEVDLVISL.IPFETLKDRLS..WIHPP.GRVYN.D
RetrocopyRLMMSELENSRGQHWLLDGFPRTLRQAEALDK>ICEVDLVISLKIPFETLKDRLSCCWIHPPRGRVYNMD
ParentalFNPPHVHGIDDVTGEPLVQQEDDKPEAVAARLRQYKDVAKPVIELYKSRGVLHQFSGTETNKIWPYVYTL
FNPPH.HGIDDVTGEPLVQ.EDDKPEA.AARLRQYK..AKPV.ELYKSRGVLHQFSGTETNKIWPYVYTL
RetrocopyFNPPHIHGIDDVTGEPLVQ*EDDKPEAAAARLRQYKYMAKPVAELYKSRGVLHQFSGTETNKIWPYVYTL
ParentalFSNKITPIQSKEAY
FSN.ITPIQSKEAY
RetrocopyFSNMITPIQSKEAY

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






(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 25 .99 RPM
SRP007412_cerebellum 0 .00 RPM 32 .95 RPM
SRP007412_heart 0 .00 RPM 21 .76 RPM
SRP007412_kidney 0 .00 RPM 108 .46 RPM
SRP007412_liver 0 .00 RPM 16 .46 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2735 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2735 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2735 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3320
Pan troglodytes retro_ptro_2154
Gorilla gorilla retro_ggor_1301
Macaca mulatta retro_mmul_2080

Parental genes homology:
Parental genes homology involve 12 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000168351 retrocopy
Homo sapiens ENSG000001624336 retrocopies
Gorilla gorilla ENSGGOG000000266444 retrocopies
Myotis lucifugus ENSMLUG000000096221 retrocopy
Macaca mulatta ENSMMUG000000010793 retrocopies
Mus musculus ENSMUSG000000285271 retrocopy
Nomascus leucogenys ENSNLEG000000151633 retrocopies
Otolemur garnettii ENSOGAG000000160241 retrocopy
Ochotona princeps ENSOPRG0000001034517 retrocopies
Pongo abelii ENSPPYG00000001269 6 retrocopies
Pongo abelii ENSPPYG000000192453 retrocopies
Pan troglodytes ENSPTRG000000008274 retrocopies



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