RetrogeneDB ID:

retro_fcat_27

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:X:81555819..81557169(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000015400
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPH1
Ensembl ID:ENSFCAG00000001204
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein H1 (H) [Source:HGNC Symbol;Acc:5041]


Retrocopy-Parental alignment summary:






>retro_fcat_27
ATGATGCTGAGCACGGAAGGCAGGGAGGGGTTCGTGGTGAAGGTCAGGGGCCTACCCTGGTCCTGCTCAGCTGATGAAGT
GATGCGCTTCTTCTCTGATTGTAAAATCCAAAATGGCACATCAGGTATTCGTTTCATCTACACCAGAGAAGGCAGACCAA
GTGGTGAAGCATTTGTCGAACTTGAATCCGAAGATGAAGTGAAATTGGCTTTGAAGAAGGACAGAGAAACCATGGGACAC
AGATATGTTGAAGTATTCAAGTCCAACAGTGTTGAAATGGATTGGGTGTTGAAGCATACAGGTCCAAATAGTCCTGATAC
TGCCAACGATGGCTTCGTCCGGCTTAGAGGACTCCCATTTGGCTGTAGCAAGGAAGAGATTGTTCAGTTCTTTTCAGGGT
TGGAAATTGTGCCAAATGGGATGACACTGCCGGTGGACTTTCAGGGGAGGAGCACAGGGGAGGCCTTTGTGCAGTTTGCT
TCACAGGAGATAGCTGAAAAGGCCTTAAAGAAACACAAGGAAAGAATAGGGCACAGGTACATTGAAATCTTCAAGAGTAG
CAGAGCTGAAGTCCGAACCCACTATGATCCCCCTCGAAAGCTCATGGCTATGCAGCGGCCAGGTCCCTATGATAGGCCAG
GGGCTGGCAGAGGGTATAATAGCATTGGCAGAGGGGCTGGGTTTGAAAGGATGAGACGTGGTGCCTATGGTGGAGGGTAT
GGAGGCTATGATGACTATGGTGGCTATAATGATGGATATGGCTTTGGGTCCGATAGGTTTGGAAGAGACCTCAATTACTG
TTTTTCAGGAATGTCTGATCATAGATATGGAGATGGTGGGTCCAGTTTCCAGAGTACCACAGGGCACTGTGTACACATGA
GGGGATTACCTTACAGAGCCACTGAGAATGATATTTACAATTTTTTCTCACCTCTTAACCCCATGAGAGTGCACATTGAA
ATTGGACCTGATGGCCGAGTTACTGGTGAGGCAGATGTTGAATTTGCTACTCATGAAGATGCTGTGGCAGCTATGGCAAA
AGACAAAGCTAATATGCAACACAGATATGTGGAGCTCTTCTTGAATTCTACTGCAGGAACGAGTGGGGGTGCTTATGATC
ACAGCTATGTAGAACTCTTTTTGAATTCTACAGCAGGGGCAAGTGGTGGTGCTTATGGTAGTCAAATGATGGGAGGGATG
GGCTTATCCAACCAGTCTAGTTATGGGGGTCCTACTAGCCAGCAGCTAAGTGGTGGCTATGGAGGTGGTTATGGTGGTCA
GAGCAGTATGAGTGGATACGACCAAGTTCTGCAGGAAAACTCCAGTGACTATCAGTCAAACCTTGCTTAA

ORF - retro_fcat_27 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.84 %
Parental protein coverage: 94.49 %
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
DRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDY.GYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
RetrocopyDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYGGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
ParentalSTFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKA
S.FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP.RVHIEIGPDGRVTGEADVEFATHEDAVAAM.KDKA
RetrocopySSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKA
ParentalNMQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGGY
NMQHRYVELFLNSTAG.SGGAY.H.YVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGP.SQQLSGGY
RetrocopyNMQHRYVELFLNSTAGTSGGAYDHSYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPTSQQLSGGY
ParentalGGGYGGQSSMSGYGSQGAVNSSYYSS
GGGYGGQSSMSGY......NSS.Y.S
RetrocopyGGGYGGQSSMSGYDQVLQENSSDYQS

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
SRP017611_brain 64 .62 RPM 186 .85 RPM
SRP017611_kidney 47 .20 RPM 293 .20 RPM
SRP017611_liver 23 .66 RPM 215 .42 RPM

ChIP-Seq - click to see more details

Felis catus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_fcat_27 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_27 was not experimentally validated.

Retrocopy orthology:
Felis catus 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 22 parental genes, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000088882 retrocopies
retro_amel_57, retro_amel_9,
Bos taurus ENSBTAG000000093891 retrocopy
retro_btau_130,
Choloepus hoffmanni ENSCHOG000000038414 retrocopies
retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus ENSCJAG000000099311 retrocopy
retro_cjac_127,
Cavia porcellus ENSCPOG000000014855 retrocopies
retro_cpor_1065, retro_cpor_1094, retro_cpor_1095, retro_cpor_121, retro_cpor_711,
Equus caballus ENSECAG000000144291 retrocopy
retro_ecab_94,
Echinops telfairi ENSETEG000000113031 retrocopy
retro_etel_50,
Felis catus ENSFCAG00000001204 2 retrocopies
retro_fcat_131, retro_fcat_27 ,
Homo sapiens ENSG000001690452 retrocopies
retro_hsap_3322, retro_hsap_4911,
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,
Otolemur garnettii ENSOGAG000000126312 retrocopies
retro_ogar_208, retro_ogar_498,
Ochotona princeps ENSOPRG000000035131 retrocopy
retro_opri_11,
Procavia capensis ENSPCAG000000067151 retrocopy
retro_pcap_4,
Pongo abelii ENSPPYG000000161211 retrocopy
retro_pabe_110,
Pteropus vampyrus ENSPVAG000000076701 retrocopy
retro_pvam_23,
Rattus norvegicus ENSRNOG000000033991 retrocopy
retro_rnor_340,
Sorex araneus ENSSARG000000030241 retrocopy
retro_sara_29,
Sarcophilus harrisii ENSSHAG000000182041 retrocopy
retro_shar_674,
Sus scrofa ENSSSCG000000140221 retrocopy
retro_sscr_70,
Vicugna pacos ENSVPAG000000074852 retrocopies
retro_vpac_594, retro_vpac_614,


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