RetrogeneDB ID:

retro_pabe_3369

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:8:128254035..128255783(-)
Located in intron of:ENSPPYG00000018849
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NCAPG
Ensembl ID:ENSPPYG00000014630
Aliases:None
Description:non-SMC condensin I complex, subunit G [Source:HGNC Symbol;Acc:24304]


Retrocopy-Parental alignment summary:






>retro_pabe_3369
ATGGTTATTTGACAGGAGATTCTTACTCTACCCACAACCCCAGTATCCCTGGTTCCTTTTCTTGTTGAAAGACTGCTCCA
CATTATTCTAGATGATAATAAGAGAACAGAATTTATCTCAGAGATTGGGGCACCCATTGTTACTGTTGGTGTTAATGATG
ACCCAGCTGATGCAAGAAAGGAAGGACTCAAGATGGCTGAAATAAAAGTTAAGCATATTGAAGCCAAAGAAGCTTTGGAA
AATTACGTTATCTTACAGGATTTTAACTCGGCATCAAAATTAAAAGAAGAAATAAGAGCATTAGAAGATGTCAAAAAACC
TTTTGCAAGAGACAGAGCAACTTGAAATTAAAGAAGTCCATGTACAGAAGAATGATGCAGAAACATTACAGAATGTCTTA
TCTTATGCTGTGAACTGTTGAAGCAGATTCCATTTCAACAGGCATAAGTGCAGCCATGAATGGGATCATTGAATTTTTTA
TTCTTCCTAAAATAATAAATGTTTACCCTATAGTAAGAAATCTGGCTGTTTTATGCTCGGGAGCTGCAGACTACAGAATC
AGAATTTTGCACATAACACTTTGTGTTATTATTGCAGGTTTTGCAAATTGATGATGTCACAATAAAAATAAGTGCTTTAA
AGGGAATCTTTGACTAGCTGATAATGTTTGGGGTTGAACCACTTAAACCTAAAAAATCAAAGCCTTTTAATATGAAGGTG
CAAAGATAAACAGTGATTAATGAGCAAGAGTCATAAAAAGTTGAAAAGGCCCTTACAGCGAAGAATGTTCTGAAACTCCT
TTCTGATTTCTTAGGTAGTGAGGTATCTACACTTAGGACAGGAGCCACAGAAGGACTAGCCAAGCTGATGTTCTCTGGGC
TTTTGGTCAGCAGCAGACTTTTTCCCATCTTATTTTGTTATGGTAGAATCCTGTGACTGAAGAGGATGTTTGACTTTGAC
ATTGCCTAGGCATGTTCTCCCCCATGTTTGCTTATGCAAGCAGGACTAATCAGAATGCTTTGAAGAAGTTTCTCTTCCAA
GCCTGCAAACACTGTCCAATGCTCCTGCATCTTCTCCTTTAGCTGAAATTGATATCAGAAATGTTGTTGAGTTACTTATA
GATTTGACAAGAACAAGTAGATTAAATCCTCAGGCCAAGAATTCCTAAGATTATCAGGCCTTAACAGTACATGACAATTT
GGCTATAAAAGTTTGCAGTGAGATCTTAAGAAGTCCACGCTCACCAGAAATTCGGGTCTCTATAAAAGCCTTGAGTTCTT
TAGAACTCAATAGCCATCTTCAAAAAGATCTTCTGGTTCTATTGAATGGGATTCTGGAGCAAGTAAAGGAGAGGGCATGT
CTGAAAGTTTTGGGGAAAGTCAAGATTCGGTTAGCAAAAAGGAAATAAAGAATTTGGTGACCAGCCTGAAGCAGCACAGG
ATGCCAGCTAGACTACAACTATTTTTCAAAATGAAGATGAAAAGAATAAGGAAGTACATATGACTCTTCTTAGGGATGTA
AAAGCAACCCTGGCATCAAAATCTACTCAACAAAAGACTAACAGTGGACAGAGAAAAGTGATAGCTTCAGCTACGATGAA
GAGAAGACATCAGATTGCTGAGGCTGACTCTGAAAGTGACCATGAAGTTCTAGAACCAGAATCAGAAATGAAGATGAAAC
TACCAAGACAAGCCAAAACAGCAGTGCTGGAAAAAAGTAAACTTAATCTTGCATAATTTCTCAATGAA

ORF - retro_pabe_3369 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.17 %
Parental protein coverage: 58.03 %
Number of stop codons detected: 10
Number of frameshifts detected 11


Retrocopy - Parental Gene Alignment:

ParentalLAVLQEILILPTIPISLVSFLVERLLHIIIDDNKRTQIVTEIISEIRAPIVTVGVNNDPADVRKKELKMA
....QEIL.LPT.P.SLV.FLVERLLHII.DDNKR....TE.ISEI.APIVTVGVN.DPAD.RK..LKMA
RetrocopyMVI*QEILTLPTTPVSLVPFLVERLLHIILDDNKR----TEFISEIGAPIVTVGVNDDPADARKEGLKMA
ParentalEIKVKLIEAKEALENCITLQDFNRASELKEEIKALEDAR-INLLKETEQLEIK-EVHTEKNDAETLQ-KC
EIKVK.IEAKEALEN...LQDFN.AS.LKEEI.ALED.......K....L..K.EVH..KNDAETLQ..C
RetrocopyEIKVKHIEAKEALENYVILQDFNSASKLKEEIRALEDVK<KTFCKRQSNLKLK<EVHVQKNDAETLQ<EC
ParentalLILCYELLKQM-SISTGLSATMNGIIESLILPGIISIHPVVRNLAVLC-LGCCGLQNQDFASK-HFVLLL
LILC.ELLKQ..SISTG.SA.MNGIIE..ILP.II...P.VRNLAVLC.LG.C.LQNQ.FA...HFVLLL
RetrocopyLILCCELLKQI<SISTGISAAMNGIIEFFILPKIINVYPIVRNLAVLC<LGSCRLQNQNFAHN<HFVLLL
ParentalQVLQIDDVTIKISALKAIFDQLMTFGIEPFKTK-KIKTLHCEGTEINSD-DEQESKEVEETATAKNVLKL
QVLQIDDVTIKISALK.IFD.L..FG.EP.K.K.KIK....EG..INSD..EQES..VE...TAKNVLKL
RetrocopyQVLQIDDVTIKISALKGIFD*LIMFGVEPLKPK<KIKAF*YEGAKINSD>NEQES*KVEKALTAKNVLKL
ParentalLSDFLDSEVCELRTGAAEGLAKLMFSGLLVSSRI-LSRLILLWYNPVTEEDVRLRHCLGVFFPVFAYASR
LSDFL.SEV..LRTGA.EGLAKLMFSGLLVSSR...S.LILLW.NPVTEEDV.L.HCLG.F.P.FAYASR
RetrocopyLSDFLGSEVSTLRTGATEGLAKLMFSGLLVSSRL<FSHLILLW*NPVTEEDV*L*HCLGMFSPMFAYASR
ParentalTNQ-ECFEEAFLPTLQTLANAPASSPLAEIDITNVAELLVDLTRPSGLNPQAKTSQDYQALTVHDNLAMK
TNQ.ECFEE..LP.LQTL.NAPASSPLAEIDI.NV.ELL.DLTR.S.LNPQAK.S.DYQALTVHDNLA.K
RetrocopyTNQ<ECFEEVSLPSLQTLSNAPASSPLAEIDIRNVVELLIDLTRTSRLNPQAKNS*DYQALTVHDNLAIK
ParentalICNEILTSPCSPEIRVYTKALSSLELSSHLAKDLLVLLNEILEQVKDRTCLRALEKIKIQL-EKGNKEFG
.C.EIL.SP.SPEIRV..KALSSLEL.SHL.KDLLVLLN.ILEQVK.R.CL..L.K.KI.L..KGNKEFG
RetrocopyVCSEILRSPRSPEIRVSIKALSSLELNSHLQKDLLVLLNGILEQVKERACLKVLGKVKIRL>QKGNKEFG
ParentalDQAEAAQDASLTTTTFQNEDEKNKEVYMTPLRGVKATQASKSTQLKTNRGQRKVTVSARTNRRHQTAEAD
DQ.EAAQDAS.TTT.FQNEDEKNKEV.MT.LR.VKAT.ASKSTQ.KTN.GQRKV..SA...RRHQ.AEAD
RetrocopyDQPEAAQDAS*TTTIFQNEDEKNKEVHMTLLRDVKATLASKSTQQKTNSGQRKVIASATMKRRHQIAEAD
ParentalSESDHEVPEPESEMKMRLPRRAKTAALEKSKLNLAQFLNE
SESDHEV.EPESEMKM.LPR.AKTA.LEKSKLNLA.FLNE
RetrocopySESDHEVLEPESEMKMKLPRQAKTAVLEKSKLNLA*FLNE

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 0 .72 RPM
SRP007412_cerebellum 0 .12 RPM 1 .95 RPM
SRP007412_heart 0 .00 RPM 0 .27 RPM
SRP007412_kidney 0 .07 RPM 0 .73 RPM
SRP007412_liver 0 .24 RPM 0 .98 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_3369 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3369 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3369 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Macaca mulatta ENSMMUG000000180701 retrocopy
retro_mmul_2370,
Nomascus leucogenys ENSNLEG000000166321 retrocopy
retro_nleu_582,
Pongo abelii ENSPPYG00000014630 1 retrocopy
retro_pabe_3369 ,


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