RetrogeneDB ID:

retro_cfam_449

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:11:21323974..21324503(-)
Located in intron of:ENSCAFG00000000948
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RNPS1
Ensembl ID:ENSCAFG00000019397
Aliases:None
Description:RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]


Retrocopy-Parental alignment summary:






>retro_cfam_449
GAGTGGAGCGAGAAGGATCTTGACAAGGATAAAACTTGGAACAAGGGCAGCACTTCCAGTGGTGGCAGCAGCACCAGGTC
CTGATCCAGCTCTACCCCCAACACCAGGACAGGCTCCAGCAGTGATTCAAGGTCCCCCCTTCAGTGTCAAGCTGCTAGGG
AAATACAGCACAACCTACAGCTCCAATTCCAGCAGCTTCTCTAGCTCAAGTACTTCTGGGCATTTGCATGACAACAGGCT
GCATTCCCATTTCAAATCCAAAACACCCAAAAGAGATGAAAAGAAAAGGAAAAAGCAGAGTCCTTCCGCTAAACCAGCTC
AAATGTCTATCAGGAGGCTCACTAGAAATGTGAGCAAGGACCACGTGATGATGATGGTCTCCACCTCTGGGAAAATTACT
ATGACTCAAATGCCTGTAGAAAGGATGTAACCCTATCTTTCTAAAGGCTATGCATCTGTGGAGTCTGAAAATCCAGATGA
AGCCAAGAAGGTGCTAAAGGACATGGACGGAGAACAAATTGATGGCCAG

ORF - retro_cfam_449 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.99 %
Parental protein coverage: 59.34 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalESSEKDRGRDKTRKRRSASSGSSSTRSRSSSTSSSGSSTSTGSSSGSSSSSASSRS-GSSSTSRSSSSSS
E.SEKD...DKT....S.SSG.SSTRS.SSST......T.TGSSS.S.S........G..ST..SS.SSS
RetrocopyEWSEKDLDKDKTWNKGSTSSGGSSTRS*SSSTPN----TRTGSSSDSRSPLQCQAA>GKYSTTYSSNSSS
ParentalSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKM
.S.S.S.S...HDNR..S..KSK.PKRDEK.RK..SPS.KP....I.RLTRNV.KDH.M...ST.GKI.M
RetrocopyFSSS-STSGHLHDNRLHSHFKSKTPKRDEKKRKKQSPSAKPAQMSIRRLTRNVSKDHVMMMVSTSGKITM
ParentalIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQ
..MPVERM.P.LSKGYA.VE.ENPDEA.K.LK.MDG.QIDGQ
RetrocopyTQMPVERM*PYLSKGYASVESENPDEAKKVLKDMDGEQIDGQ

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 0 .00 RPM 97 .77 RPM
SRP017611_brain 0 .08 RPM 73 .83 RPM
SRP017611_kidney 0 .00 RPM 35 .07 RPM
SRP017611_liver 0 .07 RPM 15 .95 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_449 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_449 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_449 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178611 retrocopy
retro_amel_194,
Bos taurus ENSBTAG000000099697 retrocopies
retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris ENSCAFG00000019397 1 retrocopy
retro_cfam_449 ,
Equus caballus ENSECAG000000232881 retrocopy
retro_ecab_524,
Felis catus ENSFCAG000000076901 retrocopy
retro_fcat_248,
Homo sapiens ENSG000002059371 retrocopy
retro_hsap_2911,
Gorilla gorilla ENSGGOG000000142751 retrocopy
retro_ggor_2016,
Macropus eugenii ENSMEUG000000088821 retrocopy
retro_meug_1996,
Myotis lucifugus ENSMLUG000000168083 retrocopies
retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta ENSMMUG000000192381 retrocopy
retro_mmul_794,
Monodelphis domestica ENSMODG000000158911 retrocopy
retro_mdom_1171,
Mus musculus ENSMUSG000000346811 retrocopy
retro_mmus_173,
Otolemur garnettii ENSOGAG000000315821 retrocopy
retro_ogar_3241,
Rattus norvegicus ENSRNOG000000087034 retrocopies
retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii ENSSHAG000000169511 retrocopy
retro_shar_390,
Ictidomys tridecemlineatus ENSSTOG000000132001 retrocopy
retro_itri_1160,
Tupaia belangeri ENSTBEG000000090988 retrocopies
retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta ENSTSYG000000016291 retrocopy
retro_tsyr_957,
Tursiops truncatus ENSTTRG000000082207 retrocopies
retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,


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