RetrogeneDB ID:

retro_apla_3

Retrocopy
location
Organism:Duck (Anas platyrhynchos)
Coordinates:KB742826.1:1027287..1029288(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAPLG00000000972
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSAPLG00000009519
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_apla_3
AGCATGGCCGGAGAGTTCGGGCTCATCCAGCTGGGCACCTACGTGGAGATCAAGCGCAGCGATGGGCGCATCCATCCAGC
GATGGTGACAGAGCTCCATGAAAGCACCTCCAGCATCACTGTGGAGTGGATCGAGAAAGGGACCAACAAGGGCAAGCAGG
TGAATCTCCAGCTTATCTTTGACCTCAACCCTCACCTGGCCCCAAGGAGCACATCCATGAGCAGCGTCGAGGCCCCGCTG
TCAGACAAAGGAGACCAGAGCCTGGTGAGCGAAGGGCAGCCACAGCCCATCAAAGTGGAGGAGCCGTCTGGAGACAGCAG
GGGCCCTGCAGGAGTCCAGCTTGGCTCCAGACCCAGGTGGGCATTACCAGGCGTGTGGCAGATTGAAAGGCTGCGAGACC
ACCGGGAACGCCGTCGGCTGGCGATGCGGGAGCAGCGAGCTCAGCAGGCCACCGCGTCGCTCCAGTCCAGGGCTGACATG
CTGGCCATGATCCAGGAGTGCCGCAGACAGCTGGACTGCGAGGCGCTGCAGGCCTCCATACCCCAGCAGCCCCATCGCAT
CTGTGTGTGTGTCCGGAAGCGGCCGCTGAACCAGCGGGAGATTGAGCTCAACGACATTGACGTGGTGACTGTGCCCTGCC
AGGACGTGGTGATGGTGCATGAAGCCAAGCAGAAGCTGGACCTCACGCAGTATCTGGACAACCAGATCTTCCGCTTTGAC
TATGTCTTTGATGACTGTGCCACCAACGAGCTGGTGTACAGGCACACTGCCCAGCCCCTGGTGGAGACCATCTTCCAGGG
GGGCATGGCCAGTTGCTTTGCCTACGGTCAGACGGGCAGCGGCAAGACACATACCATGAGGGGAGGCTTCTCTAGCAAGA
GCTCTGAGTGCTCCAAGGGGATCTACATCCTGGTTGCTGAGGACGTCTTCCGCAGGCTGAAGGATCCTAGCTGCCCAATA
CTGGAGCTTCGAGTCTATGGGGCTTTCTTTGAGATTTATGGGGGCAAAGTGTTTGACCTGCTGAACTCGAAGAAGCGGCT
GAGGGTGCTAGAAGATGGGAAGCATCAGATCCAAGTGGTGGGCCTTAGGGAGGAAGAGGTCACCAGTGTGGAAGATGTCA
GCAAACTGATTGAAATAGGCAGCAAGTGTCGCACGTCAGGCCAGACTTCTGCCAACTCTCACTCCTCCCGGAGCCATGCC
ATCTTCCAGATCATACTCAGGAAGAGGGGGTATTTGTACGCCAAGTTTTCACTGATTGATTTGGCTGGGAATGAGAGAGG
AGCTGACATCTCCACTGCAGACAGGCAAACGAGGCTGGAGGGGGCTGATATTAATAAAAGCCTCTTGGCACTCAAAGAGT
GCATCAGGGCACTGGGACATAACAAAGCCCACACCCCATTCAGGGCCAGCAAACTCACCCAGGTCCTGCGGGACTCATTT
ATCGGGGAAAACTCACGTACCTGCATGATTGCCACTGTCTCTCCAGGGATGAGATCCTGCGAGCACAGCCTTAACACCCT
GCGGTATGCCAACCGTGTGAAGGAGCTGGTGGTGAATTTAAACTCCCTTGGACAATCCCGTCAGGAGGTGCCAAGGTTCC
TGCATCGGATAAAGGACACAAAGAAACCCTGGGCTGTTCAGAACCCCTCCGGGACACCTGAGTTACAGCTGTCTGGGGTA
CAGCCTGACAAGGAGGTATCACCCCAGATATTTACTTTCAATGCCAAAGGAAAAGCGCAGAAGAAGAGAAAAGAGGCAGA
TGAGAAGGCGCTTCTGGAGGAGCATCAGGAGTCTCTGCGATGGTTGAAAGCGTTCCTACAGGTGGCCGAAGAAATAGACT
ACAATGTGGATTTTTACGCTGCACAGTTTGAATCAGTCCTGGGTCAAAAAATTGGCACCCTGACCGAGATTCAAGAAAAA
GTCAAATTATTCCGGTCAATTCTTTGCAAGGAAGAACAGGGCAGCAACCAGAGCTGCATGAAGAGATCTCGTGTGCTGTA
A

ORF - retro_apla_3 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.83 %
Parental protein coverage: 53.91 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVKEVEKLQEKREKRRLQQQELREKRAQDVDAT-NPNYEIMCMIRDFRGSLDYRPLTTAADPIDEHRICVC
V...E.L...RE.RRL.....RE.RAQ...A..........MI...R..LD...L..A..P...HRICVC
RetrocopyVWQIERLRDHRERRRLA---MREQRAQQATASLQSRADMLAMIQECRRQLDCEALQ-ASIPQQPHRICVC
ParentalVRKRPLNKKETLMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDTAPNEMVYRFTARPL
VRKRPLN..E....D.DV.T.P..DVVMVHE.KQK.DLT.YL.NQ.FRFDY.FDD.A.NE.VYR.TA.PL
RetrocopyVRKRPLNQREIELNDIDVVTVPCQDVVMVHEAKQKLDLTQYLDNQIFRFDYVFDDCATNELVYRHTAQPL
ParentalVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVYATFF
VETIF..GMA.CFAYGQTGSGKTHTM.G.FS.K...CSKGIY.L.A.DVF..LK.P....LEL.VY..FF
RetrocopyVETIFQGGMASCFAYGQTGSGKTHTMRGGFSSKSSECSKGIYILVAEDVFRRLKDPSCPILELRVYGAFF
ParentalEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIEIGNSCRTSGQTSANAHSSRSHA
EIY.GKVFDLLN.K..LRVLEDGK.Q.QVVGL.E.EV..VEDV.KLIEIG..CRTSGQTSAN.HSSRSHA
RetrocopyEIYGGKVFDLLNSKKRLRVLEDGKHQIQVVGLREEEVTSVEDVSKLIEIGSKCRTSGQTSANSHSSRSHA
ParentalVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTPFRAS
.FQIILR..G.L..KFSLIDLAGNERGAD.S.ADRQTRLEGA.INKSLLALKECIRALG.NK.HTPFRAS
RetrocopyIFQIILRKRGYLYAKFSLIDLAGNERGADISTADRQTRLEGADINKSLLALKECIRALGHNKAHTPFRAS
ParentalKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANSCRVKEFGIS
KLTQVLRDSFIGENSRTCMIAT.SPGM.SCE..LNTLRYAN..RVKE....
RetrocopyKLTQVLRDSFIGENSRTCMIATVSPGMRSCEHSLNTLRYAN--RVKELVVN

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






RNA-Seq - click to see more details

Anas platyrhynchos was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Anas platyrhynchos was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_apla_3 retrocopy.

TSS - click to see more details

Anas platyrhynchos was not studied using FANTOM5 data.

Lab - click to see more details

retro_apla_3 was not experimentally validated.

Retrocopy orthology:
Anas platyrhynchos 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 24 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Anas platyrhynchos ENSAPLG00000009519 1 retrocopy
retro_apla_3 ,
Bos taurus ENSBTAG000000150221 retrocopy
retro_btau_180,
Choloepus hoffmanni ENSCHOG000000078881 retrocopy
retro_chof_1348,
Cavia porcellus ENSCPOG000000093931 retrocopy
retro_cpor_72,
Dipodomys ordii ENSDORG000000063351 retrocopy
retro_dord_763,
Equus caballus ENSECAG000000198101 retrocopy
retro_ecab_32,
Homo sapiens ENSG000000687961 retrocopy
retro_hsap_69,
Gorilla gorilla ENSGGOG000000047741 retrocopy
retro_ggor_68,
Macaca mulatta ENSMMUG000000003991 retrocopy
retro_mmul_145,
Monodelphis domestica ENSMODG000000196051 retrocopy
retro_mdom_242,
Mus musculus ENSMUSG000000216931 retrocopy
retro_mmus_68,
Nomascus leucogenys ENSNLEG000000028651 retrocopy
retro_nleu_2329,
Oryctolagus cuniculus ENSOCUG000000104661 retrocopy
retro_ocun_156,
Otolemur garnettii ENSOGAG000000005275 retrocopies
retro_ogar_126, retro_ogar_3166, retro_ogar_3498, retro_ogar_3501, retro_ogar_672,
Ochotona princeps ENSOPRG000000117681 retrocopy
retro_opri_815,
Procavia capensis ENSPCAG000000050891 retrocopy
retro_pcap_22,
Rattus norvegicus ENSRNOG000000140002 retrocopies
retro_rnor_1284, retro_rnor_47,
Sorex araneus ENSSARG000000077681 retrocopy
retro_sara_457,
Sarcophilus harrisii ENSSHAG000000019501 retrocopy
retro_shar_30,
Ictidomys tridecemlineatus ENSSTOG000000127101 retrocopy
retro_itri_40,
Tupaia belangeri ENSTBEG000000093961 retrocopy
retro_tbel_761,
Tarsius syrichta ENSTSYG000000021151 retrocopy
retro_tsyr_1791,
Vicugna pacos ENSVPAG000000088641 retrocopy
retro_vpac_572,
Drosophila melanogaster FBgn00302682 retrocopies
retro_dmel_1, retro_dmel_2,




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