RetrogeneDB ID:

retro_fcat_915

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:B3:83010145..83010796(-)
Located in intron of:ENSFCAG00000024538
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSFCAG00000005265
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_fcat_915
GTGCCTTCACCTCTAGAGGGGTCATCCTTCTGACCCTTTGCAGACATGCTATCCAGCAACCAGTCTAGCCTAGTCAAGAT
GATGATCCACCCCCTTCCACACTATTCAAAGACTACCAGAACATTCCTGGAAATGAGAAGGCTAATGATGTCATACAAAG
ACTTGTCTTTGGAAATGGCCTACCAAAAAAGAAGCTAAAAATCAAGCAAGAGCAGTTGATGAACAAGATCATGGCAAACC
ATGAGGACACCAGTACCCTGGACACTCTAATGGTTGCCTTGACTGTCAAGATCTGCAGTTATAAAGAATATATGCATAAA
TATTGAAAGGACAAAGCCCACAAGTGCTATCTGCTGATAAGCAGCAATCAGAGGAAAAAGATGCTCAAAAACTTCCGTAA
GACCAACTATAATGTCTTTGAAAAGATATGCAAGGAGTTGGGGACTGAGTATACCTTTCTCCTCTGTACTACTGAAAAGC
TCACCACTGTGGTGACCAAGAAGGTTCTGTATATTTACGTTTTCCAGGAGGCACAAAAGCAATCAATCAATCAATAAGCA
AGCCCTAAAAGCTGCAACAGCAACCTGGAAACAAAGTCAGAAGAATCCACAGAGTCATTCCAAAGCTGGGCCAGAGGCAA
TCAAAGGAAAC

ORF - retro_fcat_915 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.93 %
Parental protein coverage: 84.56 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLPSP-PGGVILPAVRGYAIQKPVQRSQEDDLPPSTLLKDYQNIPGIEKFDDVVRRLLSLEMANQKEKLKV
.PSP...GVIL......AIQ.PV..SQ.DD.PPSTL.KDYQNIPG.EK..DV..RL........K.KLK.
RetrocopyVPSP<SRGVILLTLCRHAIQQPV*PSQDDDPPPSTLFKDYQNIPGNEKANDVIQRLVFGNGLPKK-KLKI
ParentalKQEQLMKKIVANPEDTSSLEARIVALTVKIRNYEEHRQKHRKDKTHKRYLLMSIDQRNKMLKNLRKTNYS
KQEQLM.KI.AN.EDTS.L....VALTVKI..Y.E...K..KDK.HK.YLL.S..QR.KMLKN.RKTNY.
RetrocopyKQEQLMNKIMANHEDTSTLDTLMVALTVKICSYKEYMHKY*KDKAHKCYLLISSNQRKKMLKNFRKTNYN
ParentalVFEKICRELGIEYTF-PPPYHRKAHH-RWATKKALCIRVFQEVQKLKK--QKRALKAAAAAARKQGQKNP
VFEKIC.ELG.EYTF..P.Y..KAHH..W......CI..F....K......K.ALK.AA.A..KQ.QKNP
RetrocopyVFEKICKELGTEYTF<SPLYY*KAHH<LW*PRR-FCIFTFSRRHKSNQSINKQALK-AATATWKQSQKNP
ParentalESPSRAGPEAIKEN
.S.S.AGPEAIK.N
RetrocopyQSHSKAGPEAIKGN

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 0 .11 RPM 26 .05 RPM
SRP017611_kidney 0 .00 RPM 53 .38 RPM
SRP017611_liver 0 .00 RPM 33 .16 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_915 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_915 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 19 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000014631 retrocopy
retro_amel_1564,
Canis familiaris ENSCAFG000000303901 retrocopy
retro_cfam_1939,
Callithrix jacchus ENSCJAG000000018523 retrocopies
retro_cjac_3095, retro_cjac_761, retro_cjac_859,
Cavia porcellus ENSCPOG000000108771 retrocopy
retro_cpor_430,
Dipodomys ordii ENSDORG000000075811 retrocopy
retro_dord_118,
Felis catus ENSFCAG00000005265 1 retrocopy
retro_fcat_915 ,
Homo sapiens ENSG000001168981 retrocopy
retro_hsap_1594,
Myotis lucifugus ENSMLUG000000064751 retrocopy
retro_mluc_1945,
Monodelphis domestica ENSMODG000000178131 retrocopy
retro_mdom_1094,
Mus musculus ENSMUSG000000288611 retrocopy
retro_mmus_3447,
Nomascus leucogenys ENSNLEG000000114671 retrocopy
retro_nleu_615,
Otolemur garnettii ENSOGAG000000026562 retrocopies
retro_ogar_1327, retro_ogar_16,
Pongo abelii ENSPPYG000000015371 retrocopy
retro_pabe_1310,
Pan troglodytes ENSPTRG000000005411 retrocopy
retro_ptro_1071,
Sus scrofa ENSSSCG000000263931 retrocopy
retro_sscr_1190,
Ictidomys tridecemlineatus ENSSTOG000000006081 retrocopy
retro_itri_454,
Tupaia belangeri ENSTBEG000000009584 retrocopies
retro_tbel_1633, retro_tbel_4438, retro_tbel_845, retro_tbel_882,
Tarsius syrichta ENSTSYG000000089482 retrocopies
retro_tsyr_1612, retro_tsyr_372,
Tursiops truncatus ENSTTRG000000023451 retrocopy
retro_ttru_1500,


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