RetrogeneDB ID:

retro_cint_3

Retrocopy
location
Organism:Vase tunicate (Ciona intestinalis)
Coordinates:HT000124.1:123246..124239(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCING00000000707
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCING00000004542
Aliases:None
Description:Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:F6Y1K6]


Retrocopy-Parental alignment summary:






>retro_cint_3
AAAATGGCTGATGACAAGTTTAATGTTGATAAAATTATTGCAAGTCTCCTGGAGGTACGAGGTTCAAGACCCGGCAAGAG
TGTTCAACTGAGTGAAAACGACATCAGAGGTTTATGTTTGAAATCAAGGGAAATATTCCTCAGTCAACCAATTCTATTGG
AACTTGAAGCTCCCCTTAAAATCTGCGGGGATATTCACGGCCAGTATTATGACCTTCTGCGGCTTTTTGAGTATGGAGCT
TTCCCCCCAGAGTCAAATTATCTCTTTCTTGGAGATTACGTGGACCGTGGAAAGCAATCATTGGAAACCATTGCCCTTCT
CCTCGCTTATAAGATAAAGTATCCGGAGAATTTCTTCTTACTTAGAGGCAACCATGAGTGTGCGAGCATCAATCGAATCT
ATGGTTTCTATGATGAGTGTAAGCGACGGTACAACATCAAGTTGTGGAAAACCTTCACGGATTGCTTCAACTGTCTCCCG
CTTGCTGCCATTATTGATGAGAAGATCTTCTGCTGCCACGGAGGACTCTCTCCTGATCTTCAATCCATGGAGCAGATCCG
GAGGATCATGAGACCAACCGATGTTCCAGATCAAGGGCTATTGTGTGACCTCTTGTGGTCCGATCCTGACAAGGAAGTCT
TCGGATGGGGCGAGAATGATAGAGGAGTGTCATTCACGTTTGGTGCTGAGGTTGTGGCCAAGTTTCTTCACAAGCATGAC
CTTGACCTTATATGTCGTGCTCACCAGGTTGTTGAAGATGGATATGAGTTCTTCGCCAAACGGCAAGTCGTCACTCTCTT
CTCGGCTCCTAATTATTGTGGGGAGTTTGACAACGCAGGAGCAATGATGAGCGTGGATGAAACTCTCATGTGCTCCTTCC
AGATCCTCAAGCCAGCAGATAAGAAGAAGTTCCCTTACGGGGGTTTAAACGCCGGACGCCCGGTCACTCCTCCTCGTAAT
TCAGGAAACAAACAGAAACCTGGGAAAAAATAA

ORF - retro_cint_3 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.48 %
Parental protein coverage: 98.79 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalDKLNVDKIIAMLLEVRGSRPGKNVQLSENDIRGLCLKSREIFLSQPILLELEAPLKICGDVHGQYYDLLR
DK.NVDKIIA.LLEVRGSRPGK.VQLSENDIRGLCLKSREIFLSQPILLELEAPLKICGD.HGQYYDLLR
RetrocopyDKFNVDKIIASLLEVRGSRPGKSVQLSENDIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLR
ParentalLFEYGGFPPESNYLFLGDYVDRGKQSLETIALLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRY
LFEYG.FPPESNYLFLGDYVDRGKQSLETIALLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRY
RetrocopyLFEYGAFPPESNYLFLGDYVDRGKQSLETIALLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRY
ParentalNIKLWKTFTDCFNCLPLAAIIDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKEVS
NIKLWKTFTDCFNCLPLAAIIDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKEV.
RetrocopyNIKLWKTFTDCFNCLPLAAIIDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKEVF
ParentalGWGENDRGVSFTFGPEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMS
GWGENDRGVSFTFG.EVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQ.VTLFSAPNYCGEFDNAGAMMS
RetrocopyGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQVVTLFSAPNYCGEFDNAGAMMS
ParentalVDETLMCSFQILKPSDKKKYPYGGMVSGRPVTPPRAGAAKSKPGKK
VDETLMCSFQILKP.DKKK.PYGG...GRPVTPPR....K.KPGKK
RetrocopyVDETLMCSFQILKPADKKKFPYGGLNAGRPVTPPRNSGNKQKPGKK

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






RNA-Seq - click to see more details

Ciona intestinalis was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ciona intestinalis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cint_3 retrocopy.

TSS - click to see more details

Ciona intestinalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_cint_3 was not experimentally validated.

Retrocopy orthology:
Ciona intestinalis 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 18 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000138611 retrocopy
retro_amel_1721,
Bos taurus ENSBTAG000000111982 retrocopies
retro_btau_6, retro_btau_960,
Ciona intestinalis ENSCING00000004542 1 retrocopy
retro_cint_3 ,
Callithrix jacchus ENSCJAG000000009831 retrocopy
retro_cjac_923,
Callithrix jacchus ENSCJAG000000091477 retrocopies
retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Dasypus novemcinctus ENSDNOG000000079863 retrocopies
retro_dnov_2565, retro_dnov_525, retro_dnov_872,
Dipodomys ordii ENSDORG000000104842 retrocopies
retro_dord_260, retro_dord_261,
Equus caballus ENSECAG000000172281 retrocopy
retro_ecab_853,
Echinops telfairi ENSETEG000000157211 retrocopy
retro_etel_2065,
Macropus eugenii ENSMEUG000000053231 retrocopy
retro_meug_1748,
Myotis lucifugus ENSMLUG000000106612 retrocopies
retro_mluc_15, retro_mluc_2217,
Mus musculus ENSMUSG000000044555 retrocopies
retro_mmus_2274, retro_mmus_2968, retro_mmus_3418, retro_mmus_851, retro_mmus_925,
Oryctolagus cuniculus ENSOCUG000000092752 retrocopies
retro_ocun_1232, retro_ocun_665,
Pan troglodytes ENSPTRG000000054481 retrocopy
retro_ptro_2435,
Sorex araneus ENSSARG000000005711 retrocopy
retro_sara_700,
Tupaia belangeri ENSTBEG000000138524 retrocopies
retro_tbel_1710, retro_tbel_2116, retro_tbel_2311, retro_tbel_4450,
Vicugna pacos ENSVPAG000000084111 retrocopy
retro_vpac_540,
Drosophila melanogaster FBgn00031345 retrocopies
retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,


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