RetrogeneDB ID:

retro_fcat_411

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:A2:166470955..166471830(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GAPDH
Ensembl ID:ENSFCAG00000006874
Aliases:None
Description:Glyceraldehyde-3-phosphate dehydrogenase [Source:UniProtKB/Swiss-Prot;Acc:Q9N2D5]


Retrocopy-Parental alignment summary:






>retro_fcat_411
GTCTACATGTTCCACTATGATTCCACCCGTAGCAAATTCAATGCACAGTCAGCGCTAAGAACGGGAAACCTGTCATCAAT
GGAAAGCCCATCTCCATCTTCCAGGAGCGAGATCCTGCCAACATCAAATGGGGAGACTCTGGTGCCGACTCCCCTGTGGA
GTCCAGTGGTATGTTCACCACCATGGAGAAAACTGGGGCTGACGTGAAGGGTGGAACTGAGAGGGTCATCATCTCTGCCT
CTTTTACTGATGTCCTCATGTTTGTGATGGGCGTGAACCACGAGAAGTACAACAACTCCCTCAAGCTTGTCAGCAACGCG
TCCTGCACCACCAACTGCTTAGTCCCTCTGGCCAAGGCCATCCATGACAACTCTGGCACTGTGGAAGGACTTATGACCAC
AGTCCACGACATCACTGCCAACCAGAAGACCACTGACGGCCCCTCTGGGAAGCTGTGGTGTGACGGCTGAGGGGCTGCTC
AGAACATCATCCCTGCATCTTCTGGTGCCACCAAGGCTATAGGCAAGGTCAACCCTGAGCTGAATGGGAAACTCATTTGG
CATGGCCTTCCATGTGCCCGCTGCCAACATGTCAGTTATGGATCTAATGCCACCTGGAGAAAGCTGCCAAATACAATGAC
ATCAAGAAGGTGGTGAAGCAGGCCATTGGGGGGCCCCCTCAAGGGCATCCAGGGCTCCAGTGAGGACCAGGTTGTCTCCT
ATGACTTTAACAGTAACACCCACTCTTCCACCTTTGATGCTGGGGCTGGCATTGCTCTCAAGGACCACTGTGTCAAGCTC
CTTTCCTGGTATGACAATGAATTTGACCACAGCAACTGAGTGGTAGATCTTATGGTCCACATGGCCTCCAAAGAG

ORF - retro_fcat_411 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.01 %
Parental protein coverage: 87.69 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalVYMFQYDSTHGKFHG-TVKAENGKLVINGKPITIFQERDPANIKWGDAGAEYVVESTGVFTTMEKAGAHL
VYMF.YDST..KF...TV.A.NGK.VINGKPI.IFQERDPANIKWGD.GA...VES.G.FTTMEK.GA..
RetrocopyVYMFHYDSTRSKFNA<TVSAKNGKPVINGKPISIFQERDPANIKWGDSGADSPVESSGMFTTMEKTGADV
ParentalKGGAKRVIISAPSADAPMFVMGVNHEKYDNSLKIVSNASCTTNCLAPLAKVIHDHFGIVEGLMTTVHAIT
KGG..RVIISA...D..MFVMGVNHEKY.NSLK.VSNASCTTNCL.PLAK.IHD..G.VEGLMTTVH.IT
RetrocopyKGGTERVIISASFTDVLMFVMGVNHEKYNNSLKLVSNASCTTNCLVPLAKAIHDNSGTVEGLMTTVHDIT
ParentalATQKTVDGPSGKLWRDGRGAAQNIIPASTGAAKAVGKVIPELNGKLT-GMAFRV-PTPNVSVVDLTCRLE
A.QKT.DGPSGKLW.DG.GAAQNIIPAS.GA.KA.GKV.PELNGKL..GMAF.V.P.P........C.LE
RetrocopyANQKTTDGPSGKLWCDG*GAAQNIIPASSGATKAIGKVNPELNGKLI>GMAFHV>PLPTCQLW-I*CHLE
ParentalKAAKYDDIKKVVKQASEGP-LKGILGYTEDQVVSCDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFG
KAAKY.DIKKVVKQA..GP.LKGI.G..EDQVVS.DFNS.THSSTFDAGAGIAL.DH.VKL.SWYDNEF.
RetrocopyKAAKYNDIKKVVKQAIGGP>LKGIQGSSEDQVVSYDFNSNTHSSTFDAGAGIALKDHCVKLLSWYDNEFD
ParentalYSNRVVDLMVHMASKE
.SN.VVDLMVHMASKE
RetrocopyHSN*VVDLMVHMASKE

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






(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 0 .11 RPM 1336 .30 RPM
SRP017611_kidney 0 .00 RPM 1121 .27 RPM
SRP017611_liver 0 .00 RPM 1465 .10 RPM
Felis catus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_fcat_411 retrocopy.
Felis catus was not studied using FANTOM5 data.
retro_fcat_411 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 23 parental genes, and 390 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066755 retrocopies
Ailuropoda melanoleuca ENSAMEG0000001432935 retrocopies
Canis familiaris ENSCAFG000000150774 retrocopies
Callithrix jacchus ENSCJAG000000082341 retrocopy
Cavia porcellus ENSCPOG000000263501 retrocopy
Equus caballus ENSECAG0000002205111 retrocopies
Felis catus ENSFCAG00000006874 17 retrocopies
Gorilla gorilla ENSGGOG0000000955330 retrocopies
Loxodonta africana ENSLAFG000000027803 retrocopies
Myotis lucifugus ENSMLUG0000001432018 retrocopies
Macaca mulatta ENSMMUG0000001867933 retrocopies
Monodelphis domestica ENSMODG0000001806641 retrocopies
Mustela putorius furoENSMPUG0000001689128 retrocopies
Mus musculus ENSMUSG00000057666109 retrocopies
retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Ornithorhynchus anatinus ENSOANG000000044921 retrocopy
Ochotona princeps ENSOPRG0000001251410 retrocopies
Procavia capensis ENSPCAG000000069289 retrocopies
Pteropus vampyrus ENSPVAG0000001257014 retrocopies
Rattus norvegicus ENSRNOG000000186304 retrocopies
Rattus norvegicus ENSRNOG000000306382 retrocopies
Sarcophilus harrisii ENSSHAG000000149534 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000075389 retrocopies
Xenopus tropicalis ENSXETG000000339751 retrocopy



Copyright © RetrogeneDB 2014-2017