RetrogeneDB ID:

retro_pabe_1920

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:2a:3043454..3044380(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CNN2
Ensembl ID:ENSPPYG00000009302
Aliases:CNN2, Calponin-2
Description:Calponin-2 [Source:UniProtKB/Swiss-Prot;Acc:Q5RFN6]


Retrocopy-Parental alignment summary:






>retro_pabe_1920
GTAAGCTCCACTCAGTTCAACAAGGGCCCCTCCTACAGGCTCTTGGCGGAAGTCCAGAACCGGCTTCTGTCCAGATATGA
CTCCCAGAAGGAGGTAGAGCTCCGCAGCTGGATCTAGGGACTCACCGGCGTCTCCATCGGCCCGACTTCCAGAAGGGCCT
GAAGGACGGGATTATTTTATGCACACTCATGAACAAACTGCAGCCGGGCTCAGTCCCCAAGATCAACTGCTTCAGTGTAG
AACTGCTACCAGCTAGAAAACCTCTCCAACTTCCTCAAGGCCATGGTCAGCTACAGCATGAACCCCGTGGACCTATTTGA
GGCCACGACCTGTTTGAGAGTGGGAACGTGAGGCAGGTGCAGGTGTCTCTTCTCGCCCTGGCAGGGAAGGCCAAGACTAA
GGGGCTGCAGAGAGAGGTGGACATCGGTGAGGAGTACTCAGAGAAGCAGGAGCGGAACTTCGACGACGCCACCATGAAGG
CTGGCCAATGCGTCATCGGGCTGCAGATTACCAACAAATGCGCCAGCCAGTCAGGCATGACTGTGTACGGCAGAGCATGA
GGAGGCATCTCTACGACCCCAAGAACCACTTGCTGCCCCCCGCGGACCACTCGACCATCACCCTCCAGATGGGTACAAGC
AAGTGCGCCAGCCAGGTGAGCATGGCAGCTCCCGGGACCCAGAGGCACATCTACGACACGAAGCTGGGAATCACAAGTAT
GACAACTCTTCCATGTCCCTGAAGATGGGCTACACGCTGGGCACCAACCAGAGCGGCCAGGTCTTCAGCCTGGGCCGACA
GATACACGACCCCAAGTACTGCCTGGGAGAGCAGTGGCCCACGGGGCTCCCTCGGGTGCAGGTGACTGACCGGGGCCAGG
GGAGGCCCCTCAATATCTCCCTTACTACCAAGAGGAGACCGGGTAC

ORF - retro_pabe_1920 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.85 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalMSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIGP-DFQKGLKDGTILCTLMNKLQP
.SSTQFNKGPSY.L.AEV.NRLLS.YD.QKE.ELR.WI.GLTG.SIGP.DFQKGLKDG.ILCTLMNKLQP
RetrocopyVSSTQFNKGPSYRLLAEVQNRLLSRYDSQKEVELRSWI*GLTGVSIGP<DFQKGLKDGIILCTLMNKLQP
ParentalGSVPKIN-RSMQNWHQLENLSNFIKAMVSYGMNPVDLFEA-NDLFESGNMTQVQVSLLALAGKAKTKGLQ
GSVPKIN..S..N..QLENLSNF.KAMVSY.MNPVDLFEA..DLFESGN..QVQVSLLALAGKAKTKGLQ
RetrocopyGSVPKIN>ASV*NCYQLENLSNFLKAMVSYSMNPVDLFEA<HDLFESGNVRQVQVSLLALAGKAKTKGLQ
ParentalSGVDIGVKYSEKQERNFDDATMKAGQCVIGLQ-MGTNKCASQSGMTA-YGTRRHLYDPKNHILPPMDHST
..VDIG..YSEKQERNFDDATMKAGQCVIGLQ...TN..ASQ.........RRHLYDPKNH.LPP.DHST
RetrocopyREVDIGEEYSEKQERNFDDATMKAGQCVIGLQ>LPTNAPASQA*LCT>QSMRRHLYDPKNHLLPPADHST
ParentalISLQMGTNKCASQVGMTAPGTRRHIYDTKL-GTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQIYDPKYC
I.LQMGT.KCASQV.M.APGT.RHIYDTKL.G..K.DNSSMSL.MGYT.G.NQSGQVF.LGRQI.DPKYC
RetrocopyITLQMGTSKCASQVSMAAPGTQRHIYDTKL<GNHKYDNSSMSLKMGYTLGTNQSGQVFSLGRQIHDPKYC
Parental-PQGTVADGAPSGTGDCPDPGEVPEYPPYYQEEAGY
.P...VA.GAPSG.GD.P.PGE.P.Y.PYYQEE.GY
Retrocopy<PGRAVAHGAPSGAGD*PGPGEAPQYLPYYQEETGY

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 10 .62 RPM
SRP007412_cerebellum 0 .00 RPM 3 .53 RPM
SRP007412_heart 0 .00 RPM 19 .99 RPM
SRP007412_kidney 0 .00 RPM 88 .20 RPM
SRP007412_liver 0 .00 RPM 41 .40 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1920 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1920 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1920 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000207641 retrocopy
Dipodomys ordii ENSDORG000000011411 retrocopy
Erinaceus europaeus ENSEEUG000000151711 retrocopy
Homo sapiens ENSG0000006466616 retrocopies
Gorilla gorilla ENSGGOG000000281539 retrocopies
Myotis lucifugus ENSMLUG000000131604 retrocopies
Macaca mulatta ENSMMUG000000153061 retrocopy
Mus musculus ENSMUSG000000046652 retrocopies
Nomascus leucogenys ENSNLEG000000011612 retrocopies
Otolemur garnettii ENSOGAG000000101442 retrocopies
Pongo abelii ENSPPYG000000006482 retrocopies
Pongo abelii ENSPPYG00000009302 12 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000283671 retrocopy



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