RetrogeneDB ID:

retro_pmar_26

Retrocopy
location
Organism:Lamprey (Petromyzon marinus)
Coordinates:GL497889:704..1589(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:rbb4l
Ensembl ID:ENSPMAG00000007189
Aliases:None
Description:retinoblastoma binding protein 4, like [Source:ZFIN;Acc:ZDB-GENE-030131-848]


Retrocopy-Parental alignment summary:






>retro_pmar_26
AGAATTTAGATTGAGACTCAAATTAATCATGCTGGAGAAGTTAATAGAGCTCGTTATATGCCTTAATCACACAATATCAT
CGCCACAAAGACTACTAGTGGCGAGGTCCACATTTTTGATTACTTTAAGCATCCCACAAAGCCAGCTAACGATCAAGTCA
AGCCAGATTTGAGATTATAAGGACATAAAAAAGAGGGTTTTGGTCTTGCTTGGAACCCAGTGAATGGAGGTATGCTGCTC
TCTGGCTCAGACGATGGTATTATTTGCATCTGGGATGTGAACAAACCCAATTAACTCAATAACACAATAGATCCATTGTA
TACTTTTGAGGCTCATACTCAAGTCGTGGAGGATGTTGCATGGAATTGCCATGATGGTAACTTATTCGCTAGTGTCAGTG
ATGATAAGAGACTTATTCTTTGGGACTTGAGAGACAGACAGCCCTCATCCAATATTGAAGCACACATGGCTGAAATTATG
TCAGTTGACTACTCGCCATTTGATCAGAACTTATTGGTCACTGGATCTGCTGATGGTTCAGTTGCTGTTTGGGACACAAG
AAATATCAAGAGTAAACTTTTCTCACTCAGATAGCATAAGGATGAAGTGACTTAAGTTAAATTCAGTCCAATGCTAGGAA
ACTTAATTGCATCATCAGGCGCAGATCGCAGAGTCATGGTTTGGGACTTATCAAGAATTGACAGACCTCAAACAGAGGAG
GAGAAGAGAGATGGTCCTCCTGAGTTGATGTTTGTGCACGGTGGTATGACTTCCAAGGTTTCAGATATCGCATGGAACTT
AAATGAGAAGTTAATGATGGCTTCGTGCTCAGAGGATAACATCCTGCAAGTCTGGCAAATTGCTCATGAAATCTACTATG
ATCAG

ORF - retro_pmar_26 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.5 %
Parental protein coverage: 70.35 %
Number of stop codons detected: 6
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKIEVEIKINHEGEVNRARYMPQNPYIIATKTPTSEVLVFDYTKHPSVPDPSGECNPDLRLRGHQKEGYGL
.I..E..INH.GEVNRARYMP....IIATKT...EV..FDY.KHP..P.......PDLRL.GH.KEG.GL
RetrocopyRI*IETQINHAGEVNRARYMP*SHNIIATKTTSGEVHIFDYFKHPTKP-ANDQVKPDLRL*GHKKEGFGL
ParentalSWNPNLSGHLLSASDDHTVCLWDISGTPREGKVVEAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLM
.WNP...G.LLS.SDD...C.WD................F..HT.VVEDV.W......LF.SV.DD..L.
RetrocopyAWNPVNGGMLLSGSDDGIICIWDVNKPN*LNNTIDPLYTFEAHTQVVEDVAWNCHDGNLFASVSDDKRLI
ParentalIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADQTVALWDLRNLKLKLHSFESHRDEIFQV
.WD.R......PS....AH.AE.......P.....L.TGSAD..VA.WD.RN.K.KL.S...H.DE...V
RetrocopyLWDLRDR---QPSSNIEAHMAEIMSVDYSPFDQNLLVTGSADGSVAVWDTRNIKSKLFSLR*HKDEVT*V
ParentalQWSPHNETILASSGTDRRLNVWDLSKIGEEQAAEDVEDGPPELLFVHGGHTAKISDFSWNPNEPWVICSV
..SP......ASSG.DRR..VWDLS.I...Q..E...DGPPEL.FVHGG.T.K.SD..WN.NE.....S.
RetrocopyKFSPMLGNLIASSGADRRVMVWDLSRIDRPQTEEEKRDGPPELMFVHGGMTSKVSDIAWNLNEKLMMASC
ParentalSEDNIMQVWQMAENIYNDE
SEDNI.QVWQ.A..IY.D.
RetrocopySEDNILQVWQIAHEIYYDQ

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






RNA-Seq - click to see more details

Petromyzon marinus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Petromyzon marinus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pmar_26 retrocopy.

TSS - click to see more details

Petromyzon marinus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pmar_26 was not experimentally validated.

Retrocopy orthology:
Petromyzon marinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 36 parental genes, and 94 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000028201 retrocopy
retro_btau_1579,
Bos taurus ENSBTAG000000059042 retrocopies
retro_btau_1610, retro_btau_630,
Canis familiaris ENSCAFG000000105271 retrocopy
retro_cfam_1550,
Choloepus hoffmanni ENSCHOG000000040666 retrocopies
retro_chof_1382, retro_chof_1649, retro_chof_1867, retro_chof_2116, retro_chof_2327, retro_chof_908,
Callithrix jacchus ENSCJAG000000010217 retrocopies
retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus ENSCPOG000000153523 retrocopies
retro_cpor_154, retro_cpor_27, retro_cpor_899,
Equus caballus ENSECAG000000227841 retrocopy
retro_ecab_767,
Echinops telfairi ENSETEG000000200084 retrocopies
retro_etel_1088, retro_etel_1462, retro_etel_1877, retro_etel_676,
Felis catus ENSFCAG000000270171 retrocopy
retro_fcat_1507,
Homo sapiens ENSG000001625216 retrocopies
retro_hsap_1305, retro_hsap_2675, retro_hsap_2814, retro_hsap_3292, retro_hsap_3600, retro_hsap_3601,
Gorilla gorilla ENSGGOG000000113134 retrocopies
retro_ggor_1022, retro_ggor_1314, retro_ggor_1867, retro_ggor_2428,
Macropus eugenii ENSMEUG000000143791 retrocopy
retro_meug_1032,
Myotis lucifugus ENSMLUG000000007492 retrocopies
retro_mluc_2275, retro_mluc_892,
Macaca mulatta ENSMMUG000000099401 retrocopy
retro_mmul_75,
Monodelphis domestica ENSMODG000000174156 retrocopies
retro_mdom_1542, retro_mdom_1833, retro_mdom_1873, retro_mdom_1900, retro_mdom_563, retro_mdom_765,
Mustela putorius furoENSMPUG000000152141 retrocopy
retro_mputfur_104,
Mus musculus ENSMUSG000000313531 retrocopy
retro_mmus_3529,
Mus musculus ENSMUSG000000572361 retrocopy
retro_mmus_356,
Nomascus leucogenys ENSNLEG000000028056 retrocopies
retro_nleu_1061, retro_nleu_1179, retro_nleu_1194, retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Oryctolagus cuniculus ENSOCUG000000006831 retrocopy
retro_ocun_1939,
Otolemur garnettii ENSOGAG000000116322 retrocopies
retro_ogar_3079, retro_ogar_3297,
Otolemur garnettii ENSOGAG000000149951 retrocopy
retro_ogar_2220,
Procavia capensis ENSPCAG000000110301 retrocopy
retro_pcap_116,
Petromyzon marinus ENSPMAG00000007189 1 retrocopy
retro_pmar_26 ,
Pongo abelii ENSPPYG000000015886 retrocopies
retro_pabe_1093, retro_pabe_2210, retro_pabe_2720, retro_pabe_2958, retro_pabe_3529, retro_pabe_3611,
Pan troglodytes ENSPTRG000000217025 retrocopies
retro_ptro_1802, retro_ptro_1909, retro_ptro_2226, retro_ptro_2987, retro_ptro_896,
Pteropus vampyrus ENSPVAG000000109812 retrocopies
retro_pvam_1094, retro_pvam_902,
Rattus norvegicus ENSRNOG000000051571 retrocopy
retro_rnor_1182,
Rattus norvegicus ENSRNOG000000214921 retrocopy
retro_rnor_1270,
Sorex araneus ENSSARG000000080793 retrocopies
retro_sara_308, retro_sara_571, retro_sara_602,
Sarcophilus harrisii ENSSHAG000000109231 retrocopy
retro_shar_399,
Ictidomys tridecemlineatus ENSSTOG000000120111 retrocopy
retro_itri_1168,
Tupaia belangeri ENSTBEG000000022363 retrocopies
retro_tbel_1360, retro_tbel_1718, retro_tbel_3802,
Tupaia belangeri ENSTBEG000000101512 retrocopies
retro_tbel_3031, retro_tbel_4341,
Tarsius syrichta ENSTSYG000000023854 retrocopies
retro_tsyr_1608, retro_tsyr_1838, retro_tsyr_1957, retro_tsyr_427,
Vicugna pacos ENSVPAG000000118764 retrocopies
retro_vpac_333, retro_vpac_419, retro_vpac_652, retro_vpac_94,




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