RetrogeneDB ID:

retro_pabe_956

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:12:106730369..106731647(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KRT18
Ensembl ID:ENSPPYG00000004563
Aliases:None
Description:keratin 18 [Source:HGNC Symbol;Acc:6430]


Retrocopy-Parental alignment summary:






>retro_pabe_956
ATGAACTTCACCACTCGCTCCACCTTCTCCACCAACTACTGGTCCCTGGGCTCTGTCCAGGCACCCAGCTATGGCACCTG
GCCGGTCAGCAGCGCGGCCAGCGTCTATGCAGGCAGCAGGGGCTCTGGTTCCTGGATCTCTGTGTCCTGCTTCATCAGCT
TCCGGGCTGCATGGAGTCCAGGGGCCTGGCCGTGGAGATGGCTGGGGGTCTGGCAGGAATGGGAGGTATCCAGAATGAGA
AGGAGACCATGCAAAGCCTGAACGACTGCCTGGACTCCTACCTGGACAGAGTGAGGAGCCTGGAGACCAAGAATCAGAAG
CTGGAGAGCAAAATCCGGGAGCACCTGGAGAAGAAGGGACCCCAGGTCAGAGACTGGAGCCATTACTTCAAGATCATCGA
TGACCTGAGGGCTCAGATCTTTGCAAACACTGTGGACAATGCCTGCATTGTTCTGCAGATCGACAAATGTCTGTCTTGCT
GCTGATGACTTTAGGGTCAAGTATGAGACAGAGCTGGCCATGGCCCATGACATCCATGGGCTCTGCAAGGTCATTGTTGA
CACCAATGTCACTCGGCTGCAGCTGGAGACAGAGATTGAGGCTCTCAAGGAGGAGCTGCTCTTCATAAAGAAGAACCACA
AAGAGGAAGTAAAAGGCCTACAAGCCCAGATTGCCAGCTCTGGGTTGACTATGGAGGTAGATGCCCTCAAATCTCAGGAC
CTTGCCAAGATCATGGCAGACATCTGGGCCCAATATGACGAGCTGGCTCGGAAGAACCAAGAGGGGCTGGACAAATACTG
GTCTCAGAAGAATTGAGGAAATCACCAAAGTGGTCACCACGCAGCCCACTGAGGTTGGAGCTACTGAGATGACGCTCACA
GAGCTGAGACGTACACTCCAGTCCTTGGAGGTTGACCTGGATTCCATGAGAAATCTGAAGGCCAGCTTGGAGGACAGCCT
GAGGGAGGTGGAGGCCCGCCACGCCCTGCAGATGGAGCAGCTCAACGGGATCCTGCTGCACCTGGAGTCAGAGCTGGCAC
AGACCCTGGAAGAGGGACAGCGCCAGGCCCAGGAGTACGAGGCCCTGCTGAACATCAAGGTCAAGCTAGGGGCTGAGATC
GACACCTACCCCTGCCTGGGGGAAGATGGCAAGGAGTTCAATCTTGGTGATGCCCTGGACAGCAGCAACTCCATGCAAAC
CATCCAAAAGACCACCACCGCCGGATAGTGGATGGCAAAGTGCTGTCTGAGACAAAGGACACCAAAGTTCTGAGGCAT

ORF - retro_pabe_956 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.02 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMNFTTRSTFSTNYRSLGSVQAPSYGARPVSSAASVYAGAGGSGSRISVSRSTSFR-GGMGSGGLATGIAG
MNFTTRSTFSTNY.SLGSVQAPSYG..PVSSAASVYAG..GSGS.ISVS...SFR.G.M.S.GLA...AG
RetrocopyMNFTTRSTFSTNYWSLGSVQAPSYGTWPVSSAASVYAGSRGSGSWISVSCFISFR<GCMESRGLAVEMAG
ParentalGLAGMGGIQNEKETMQSLNDRLASYLDRVRSLETENRRLESKIREHLEKKGPQVRDWSHYFKIIEDLRAQ
GLAGMGGIQNEKETMQSLND.L.SYLDRVRSLET.N..LESKIREHLEKKGPQVRDWSHYFKII.DLRAQ
RetrocopyGLAGMGGIQNEKETMQSLNDCLDSYLDRVRSLETKNQKLESKIREHLEKKGPQVRDWSHYFKIIDDLRAQ
ParentalIFANTVDNARIVLQID-NARLAADDFRVKYETELAMRQSVENDIHGLRKVIDDTNVTRLQLETEIEALKE
IFANTVDNA.IVLQID.N..LAADDFRVKYETELAM......DIHGL.KVI.DTNVTRLQLETEIEALKE
RetrocopyIFANTVDNACIVLQID>NVCLAADDFRVKYETELAMA----HDIHGLCKVIVDTNVTRLQLETEIEALKE
ParentalELLFMKKNHEEEVKGLQAQIASSGLTVEVDAPKSQDLAKIMADIRAQYDELARKNREELDKYWSQQ-IEE
ELLF.KKNH.EEVKGLQAQIASSGLT.EVDA.KSQDLAKIMADI.AQYDELARKN.E.LDKYWSQ..IEE
RetrocopyELLFIKKNHKEEVKGLQAQIASSGLTMEVDALKSQDLAKIMADIWAQYDELARKNQEGLDKYWSQK>IEE
ParentalSTTVVTTQSAEVGAAETTLTELRRTVQSLEIDLDSMRNLKASLENSLREVEARYALQMEQLNGILLHLES
.T.VVTTQ..EVGA.E.TLTELRRT.QSLE.DLDSMRNLKASLE.SLREVEAR.ALQMEQLNGILLHLES
RetrocopyITKVVTTQPTEVGATEMTLTELRRTLQSLEVDLDSMRNLKASLEDSLREVEARHALQMEQLNGILLHLES
ParentalELAQTRAEGQRQAQEYEALLNIKVKLEAEIATYRRLLEDGEDFNLGDALDSSNSMQTIQKTTT-RRIVDG
ELAQT..EGQRQAQEYEALLNIKVKL.AEI.TY..L.EDG..FNLGDALDSSNSMQTIQKTTT.RRIVDG
RetrocopyELAQTLEEGQRQAQEYEALLNIKVKLGAEIDTYPCLGEDGKEFNLGDALDSSNSMQTIQKTTT<RRIVDG
ParentalKVVSETNDTKVLRH
KV.SET.DTKVLRH
RetrocopyKVLSETKDTKVLRH

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 2 .05 RPM
SRP007412_cerebellum 0 .00 RPM 6 .20 RPM
SRP007412_heart 0 .00 RPM 1 .29 RPM
SRP007412_kidney 0 .00 RPM 50 .15 RPM
SRP007412_liver 0 .00 RPM 198 .51 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_956 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_956 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_956 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1153
Pan troglodytes retro_ptro_787
Gorilla gorilla retro_ggor_898

Parental genes homology:
Parental genes homology involve 21 parental genes, and 338 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000119812 retrocopies
Canis familiaris ENSCAFG0000000715410 retrocopies
Callithrix jacchus ENSCJAG0000001816529 retrocopies
Cavia porcellus ENSCPOG000000026181 retrocopy
Echinops telfairi ENSETEG000000081301 retrocopy
Homo sapiens ENSG0000011105760 retrocopies
Gorilla gorilla ENSGGOG0000001015728 retrocopies
Macropus eugenii ENSMEUG0000001226214 retrocopies
Myotis lucifugus ENSMLUG000000224398 retrocopies
Macaca mulatta ENSMMUG000000319114 retrocopies
Mustela putorius furoENSMPUG000000063692 retrocopies
Mus musculus ENSMUSG000000230432 retrocopies
Nomascus leucogenys ENSNLEG0000001773245 retrocopies
Oryctolagus cuniculus ENSOCUG000000276911 retrocopy
Pongo abelii ENSPPYG00000004563 60 retrocopies
Pan troglodytes ENSPTRG0000000499658 retrocopies
Pteropus vampyrus ENSPVAG000000093612 retrocopies
Rattus norvegicus ENSRNOG000000473933 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000155873 retrocopies
Tursiops truncatus ENSTTRG000000129772 retrocopies
Vicugna pacos ENSVPAG000000074213 retrocopies



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