RetrogeneDB ID:

retro_cfam_140

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:8:38967399..38969313(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000016031
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000011666
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_140
ATGTCTGCCCGCGGCCCGGCTATCGGCATCGACCTGGGCACCACGTACTCGTGCGTCGGGGTCTTCCAACACGGCAAAGT
AGAGATCATCGCCAACGACCAGGGCAACCGCACCACCCCCAGCTACGTGGCCTTCACCGACACGGAGCGCCTCATCGGCG
ACGCCGCCAAGAACCAGGTGGCCATGAACCCCACCAACACCATCTTCGACGCCAAGAGGCTGATCGGGCGGAAGTTCGAG
GACGCCACGGTGCAATCGGACATGAAACACTGGCCGTTCCGGGTGGTGAGCGAGGGAGGGAAACCCAAGGTGCAGGTGGA
GTACAAGGGAGAGATGAAGACCTTCTTCCCGGAGGAGATCTCCTCCATGGTCCTCACGAAGATGAAGGAGATCGCCGAAG
CCTATCTGGGGGGCAAGGTGCAGAGCGCGGTCATCACGGTCCCGGCTTACTTCAATGACTCGCAGCGCCAGGCCACCAAG
GATGCGGGCACCATCACCGGCCTCAACGTGCTGCGCATCATCAACGAGCCGACCGCCGCGGCCATTGCCTACGGCCTGGA
CAAGAAGGGGTGCGCCGGCGGCGAGAAGAACGTGCTCATCTTTGACCTGGGCGGCGGCACCTTCGACGTGTCCATCCTGA
CCATCGAGGACGGCATCTTCGAGGTGAAGTCCACAGCCGGCGACACCCACCTGGGCGGCGAGGACTTCGACAACCGCATG
GTGAGCCACCTGGCGGAGGAGTTCAAGCGCAAGCACAAGAAGGACATTGGGCCCAACAAGCGCGCAGTGCGGCGACTGCG
CACCGCCTGCGAGCGCGCCAAGCGCACCTTGAGCTCGTCGACGCAGGCGAGCATCGAGATCGACTCGCTGTACGAGGGCG
TGGACTTCTACACGTCCATCACCCGCGCCCGCTTCGAAGAGCTCAACGCGGACCTCTTCCGCGGAACCCTGGAGCCGGTG
GAGAAGGCGCTGCGTGACGCCAAGCTGGACAAGGGCCAGATCCAGGAGATCGTGCTGGTGGGCGGCTCCACCCGCATCCC
CAAGATCCAGAAGCTGTTACAGGATTTCTTCAACGGCAAGGAGCTGAACAAGAGCATCAACCCCGACGAGGCGGTGGCCT
ACGGAGCCGCGGTGCAGGCGGCCATCCTCATCGGGGACAAGTCGGAGAACGTGCAGGACCTGCTGCTGCTCGACGTGACC
CCCTTGTCGTTGGGCATTGAGACGGCTGGCGGCGTCATGACCCCACTCATCAAGAGGAACACCACGATCCCGACCAAGCA
AACGCAGACCTTCACCACCTACTCAGACAACCAGAGCAGCGTGCTGGTGCAGGTGTACGAGGGCGAGCGGGCCATGACCA
AGGACAATAACCTGCTGGGCAAGTTCGACCTGACCGGGATTCCCCCGGCTCCCCGCGGGGTCCCCCAGATCGAGGTCACC
TTCGACATCGACGCCAACGGCATCCTCAACGTCACCGCCGCCGACAAGAGCACCGGTAAAGAAAACAAAATTACCATTAC
CAACGACAAGGGTCGTCTAAGCAAGGACGACATTGACCGGATGGTGCAGGAGGCCGAGCGGTACAAGTCGGAAGATGAAG
CCAATCGCGACCGGGTCGCCGCCAAAAACGCGGTGGAGTCCTATACCTACAACATCAAGCAGACGGTGGAAGACGAGAAA
CTCAGGGGCAAGATTAGCGAGCAGGACAAAAACAAGATCCTCGACAAGTGTCAGGAGGTGATCAACTGGCTCGACCGAAA
CCAGATGGCAGAGAAAGACGAGTATGAACACAAGCAGAAAGAGCTTGAAAGAGTGTGCAACCCCATCATCAGCAAACTTT
ACCAAGGCGGCCCTGGCGGCGGCGGCGGCGGTTCTGGAGCCTCCGGGGGACCGACCATCGAGGAAGTGGACTAA

ORF - retro_cfam_140 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.39 %
Parental protein coverage: 97.52 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAK
..GPA.GIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNT.FDAK
RetrocopyARGPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTIFDAK
ParentalRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTN
RLIGR.F.DA.VQSDMKHWPF.VV...G.PKVQVEYKGE.K.F.PEE.SSMVLTKMKEIAEAYLG..V..
RetrocopyRLIGRKFEDATVQSDMKHWPFRVVSEGGKPKVQVEYKGEMKTFFPEEISSMVLTKMKEIAEAYLGGKVQS
ParentalAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKK--VGAERNVLIFDLGGGTFDVSI
AV.TVPAYFNDSQRQATKDAGTI.GLNVLRIINEPTAAAIAYGLDKK...G.E.NVLIFDLGGGTFDVSI
RetrocopyAVITVPAYFNDSQRQATKDAGTITGLNVLRIINEPTAAAIAYGLDKKGCAGGEKNVLIFDLGGGTFDVSI
ParentalLTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQ
LTIEDGIFEVKSTAGDTHLGGEDFDNRMV.H...EFKRKHKKDI..NKRAVRRLRTACERAKRTLSSSTQ
RetrocopyLTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDIGPNKRAVRRLRTACERAKRTLSSSTQ
ParentalASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKL
ASIEIDSLYEG.DFYTSITRARFEELNADLFRGTL.PVEKALRDAKLDK.QI..IVLVGGSTRIPKIQKL
RetrocopyASIEIDSLYEGVDFYTSITRARFEELNADLFRGTLEPVEKALRDAKLDKGQIQEIVLVGGSTRIPKIQKL
ParentalLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTT
LQDFFNGKELNKSINPDEAVAYGAAVQAAIL.GDKSENVQDLLLLDVTPLSLGIETAGGVMT.LIKRNTT
RetrocopyLQDFFNGKELNKSINPDEAVAYGAAVQAAILIGDKSENVQDLLLLDVTPLSLGIETAGGVMTPLIKRNTT
ParentalIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
IPTKQTQTFTTYSDNQ..VL.QVYEGERAMTKDNNLLGKF.LTGIPPAPRGVPQIEVTFDIDANGILNV.
RetrocopyIPTKQTQTFTTYSDNQSSVLVQVYEGERAMTKDNNLLGKFDLTGIPPAPRGVPQIEVTFDIDANGILNVT
ParentalAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQ
A.DKSTGKENKITITNDKGRLSK.DI.RMVQEAE.YK.EDE..RD.V..KN..ESY..N.K.TVEDEKL.
RetrocopyAADKSTGKENKITITNDKGRLSKDDIDRMVQEAERYKSEDEANRDRVAAKNAVESYTYNIKQTVEDEKLR
ParentalGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGFPGGG
GKI...DK.KILDKC.E.INWLD.NQ.AEK.E.EH.QKELE.VCNPII.KLYQ...G.PGG..GG....G
RetrocopyGKISEQDKNKILDKCQEVINWLDRNQMAEKDEYEHKQKELERVCNPIISKLYQ---GGPGGGGGGSGASG
ParentalAP
.P
RetrocopyGP

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
SRP012049_cerebellum 73 .41 RPM 374 .92 RPM
SRP017611_brain 22 .63 RPM 810 .44 RPM
SRP017611_kidney 26 .68 RPM 1005 .22 RPM
SRP017611_liver 5 .66 RPM 518 .62 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

18 EST(s) were mapped to retro_cfam_140 retrocopy
EST ID Start End Identity Match Mis-match Score
BM537533 38968008 38968620 99.6 609 3 606
BM539372 38967792 38968255 99.8 462 1 461
DN341595 38968069 38968598 99.9 528 1 527
DN367982 38967320 38967748 98.1 412 8 404
DN368588 38967303 38967951 100 648 0 648
DN374967 38967305 38968006 99.8 699 2 697
DN375568 38967314 38968040 100 726 0 726
DN401772 38967309 38967903 100 594 0 594
DN402373 38967304 38967888 100 584 0 584
DN420719 38967310 38968001 99.9 690 1 689
DN425379 38967314 38968062 99.8 742 2 737
DN441303 38967321 38967859 99.5 535 3 532
DN441661 38967303 38967811 99.7 506 2 504
DN441997 38967317 38967896 100 579 0 579
DN442386 38967788 38968395 100 607 0 607
DN442567 38967305 38967921 100 616 0 616
DN444538 38967342 38967809 99.8 466 1 465
DN874941 38967734 38968362 99.9 626 0 624

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_140 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_140 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_68
Gorilla gorilla retro_ggor_1053
Pongo abelii retro_pabe_183
Bos taurus retro_btau_354
Parental genes homology:
Parental genes homology involve 35 parental genes, and 119 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca ENSAMEG000000084251 retrocopy
retro_amel_126,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Bos taurus ENSBTAG000000131621 retrocopy
retro_btau_354,
Canis familiaris ENSCAFG00000011666 3 retrocopies
retro_cfam_140 , retro_cfam_191, retro_cfam_509,
Ciona intestinalis ENSCING000000096651 retrocopy
retro_cint_12,
Callithrix jacchus ENSCJAG000000076485 retrocopies
retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Dipodomys ordii ENSDORG000000154671 retrocopy
retro_dord_16,
Equus caballus ENSECAG000000135102 retrocopies
retro_ecab_291, retro_ecab_628,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Felis catus ENSFCAG000000011326 retrocopies
retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens ENSG000001099718 retrocopies
retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Gorilla gorilla ENSGGOG000000083818 retrocopies
retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Loxodonta africana ENSLAFG000000303124 retrocopies
retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Macaca mulatta ENSMMUG000000046967 retrocopies
retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 retrocopies
retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Mus musculus ENSMUSG000000156568 retrocopies
retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Nomascus leucogenys ENSNLEG000000074198 retrocopies
retro_nleu_119, retro_nleu_1258, retro_nleu_1261, retro_nleu_1582, retro_nleu_175, retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Oryctolagus cuniculus ENSOCUG000000155334 retrocopies
retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pongo abelii ENSPPYG000000039879 retrocopies
retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Pan troglodytes ENSPTRG000000044045 retrocopies
retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Ictidomys tridecemlineatus ENSSTOG000000037561 retrocopy
retro_itri_51,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Tursiops truncatus ENSTTRG000000111396 retrocopies
retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,


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