RetrogeneDB ID:

retro_cfam_200

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:X:75324480..75325830(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000017693
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPH1
Ensembl ID:ENSCAFG00000000336
Aliases:HNRNPH1, HNRPH1
Description:heterogeneous nuclear ribonucleoprotein H1 (H) [Source:HGNC Symbol;Acc:5041]


Retrocopy-Parental alignment summary:






>retro_cfam_200
ATGATGCTGAGCACGGAAGGCAGGGAGGGGTTCGTGGTGAAGGTCAGGGGCCTACCCTGGTCCTGCTCAGCTGATGAAGT
GATGCGCTTCTTCTCTGATTGCAAGATCCAAAACGGCACATCAGGTATTCGTTTCATCTATACCAGAGAAGGCAGACCAA
GTGGTGAAGCGTTTGTCGAACTTGAATCCGAAGATGAAGTGAAATTGGCATTGAAGAAGGACAGAGAAACCATGGGACAC
AGATACGTTGAAGTGTTCAAGTCCAACAGTGTTGAAATGGATTGGGTGTTGAAGCATACAGGTCCGAATAGTCCTGATAC
TGCCAACGATGGCTTCGTCCGGCTTAGAGGACTCCCATTTGGCTGTAGCAAGGAAGAGATTGTTCAGTTCTTTTCAGGGT
TGGAAATTGTGCCAAATGGGATGACACTGCCGGTGGACTTTCAGGGGCGGAGCACGGGGGAGGCCTTTGTGCAGTTTGCT
TCGCAGGAGATAGCTGAAAAGGCCTTAAAGAAACACAAGGAAAGAATAGGGCATAGGTACATTGAAATCTTCAAGAGTAG
CCGAGCTGAAGTCCGAACCCACTACGACCCCCCGCGAAAGCTCATGGCTATGCAGCGGCCAGGTCCTTATGATAGGCCAG
GGGCTGGCAGAGGGTATAATAGTATTGGCAGAGGGACTGGGTTTGAAAGGATGAGGCGTGGTGCCTATGGTGGAGGGTAT
GGAGGCTATGATGACTATGGTGGCTATAATGATGGCTATGGCTTTGGGTCTGATAGATTTGGAAGAGACCTCAATTACTG
TTTTTCAGGGATGTCTGACCATAGATATGGAGATGGTGGGTCCAGTTTCCAGAGCACCACAGGGCACTGTGTACACATGA
GGGGATTACCTTACAGAGCCACTGAGAATGATATTTACAATTTTTTCTCACCTCTTAACCCCATGAGAGTGCACATTGAA
ATTGGACCCGATGGCCGAGTTACTGGTGAGGCAGATGTTGAATTTGCTACCCATGAAGATGCTGTGGCAGCTATGGCAAA
AGACAAAGCTAATATGCAACACAGATACGTGGAGCTCTTCTTGAATTCTACTGCAGGAACAAGTGGGGGTGCTTATGATC
ACAGCTATGTAGAACTCTTTTTGAATTCTACAGCAGGGGCAAGTGGTGGTGCATATGGTAGTCAAATGATGGGAGGAATG
GGCTTATCCAACCAATCTAGTTATGGGGGCCCTGCCAGCCAGCAGCTAAGCGGGGGTTATGGAGGTGGGTACGGTGGTCA
GAGCAGTATGAGTGGATATGACCAAGTGCTGCAGGAAAACTCCAGTGACTATCAGTCAAACCTCGCTTAA

ORF - retro_cfam_200 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.36 %
Parental protein coverage: 95.44 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMMLGTEGGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLA
MML.TEG.EGFVVKVRGLPWSCSADEV.RFFSDCKIQNG..GIRFIYTREGRPSGEAFVELESEDEVKLA
RetrocopyMMLSTEGREGFVVKVRGLPWSCSADEVMRFFSDCKIQNGTSGIRFIYTREGRPSGEAFVELESEDEVKLA
ParentalLKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
LKKDRETMGHRYVEVFKSN.VEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
RetrocopyLKKDRETMGHRYVEVFKSNSVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
ParentalITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
.TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
RetrocopyMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
ParentalDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
DRPGAGRGYNSIGRG.GFERMRRGAYGGGYGGYDDY.GYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
RetrocopyDRPGAGRGYNSIGRGTGFERMRRGAYGGGYGGYDDYGGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
ParentalSTFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKA
S.FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP.RVHIEIGPDGRVTGEADVEFATHEDAVAAM.KDKA
RetrocopySSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKA
ParentalNMQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYANQSSYGGPASQQLSGGYGGGYGGQSS
NMQHRYVELFLNSTAG.SGGAY.H.YVELFLNSTAGASGGAY..Q...G...S.Q.S..YGG....Q.S
RetrocopyNMQHRYVELFLNSTAGTSGGAYDHSYVELFLNSTAGASGGAYGSQMMGGMGLSNQSS--YGGPASQQLS

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 78 .08 RPM 330 .78 RPM
SRP017611_brain 55 .26 RPM 127 .90 RPM
SRP017611_kidney 45 .96 RPM 135 .71 RPM
SRP017611_liver 18 .78 RPM 131 .61 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_cfam_200 retrocopy
EST ID Start End Identity Match Mis-match Score
CO664956 75324543 75325003 99.6 458 2 456

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_200 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_200 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000093891 retrocopy
retro_btau_130,
Canis familiaris ENSCAFG00000000336 2 retrocopies
retro_cfam_200 , retro_cfam_230,
Canis familiaris ENSCAFG000000093051 retrocopy
retro_cfam_1096,
Choloepus hoffmanni ENSCHOG000000038414 retrocopies
retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus ENSCJAG000000099311 retrocopy
retro_cjac_127,
Dipodomys ordii ENSDORG000000054531 retrocopy
retro_dord_3,
Equus caballus ENSECAG000000144291 retrocopy
retro_ecab_94,
Echinops telfairi ENSETEG000000113031 retrocopy
retro_etel_50,
Gorilla gorilla ENSGGOG000000258442 retrocopies
retro_ggor_1299, retro_ggor_177,
Myotis lucifugus ENSMLUG000000166251 retrocopy
retro_mluc_124,
Macaca mulatta ENSMMUG000000108431 retrocopy
retro_mmul_2,
Monodelphis domestica ENSMODG000000094363 retrocopies
retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Mustela putorius furoENSMPUG000000006931 retrocopy
retro_mputfur_156,
Mus musculus ENSMUSG000000078501 retrocopy
retro_mmus_142,
Nomascus leucogenys ENSNLEG000000266583 retrocopies
retro_nleu_1668, retro_nleu_28, retro_nleu_48,
Ochotona princeps ENSOPRG000000035131 retrocopy
retro_opri_11,
Procavia capensis ENSPCAG000000067151 retrocopy
retro_pcap_4,
Pteropus vampyrus ENSPVAG000000076701 retrocopy
retro_pvam_23,
Sorex araneus ENSSARG000000030241 retrocopy
retro_sara_29,
Sarcophilus harrisii ENSSHAG000000182041 retrocopy
retro_shar_674,
Ictidomys tridecemlineatus ENSSTOG000000163762 retrocopies
retro_itri_66, retro_itri_78,
Vicugna pacos ENSVPAG000000074852 retrocopies
retro_vpac_594, retro_vpac_614,




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