RetrogeneDB ID:

retro_cint_33

Retrocopy
location
Organism:Vase tunicate (Ciona intestinalis)
Coordinates:HT000550.1:1833..2571(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCING00000018826
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCING00000006860
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cint_33
TCGCAACAACTGGCTACAGAGGAAAGATTCATCAGCGAACCAAATAATGAAACTCCGGGCCAAGCTCGCAAGTCGTTGAG
CAAAAAGACAAAACCACAGAAGCCAAGAACGAAGAATCTGCTCCCAGCACACAACCACCTGAAATTAAACTAGTCAAACA
CAACCTGAAAAGTGGAAGCAGTGATACATCAAAATCAGAACGCGAAAAAAAGCTGAAACTTGACCGTGAAAAGCGACCCA
GGGAAATAGCTTTAGCTTCAAAGGTCTGGTTGTCCAAGTCACCAAGAGGTCTTTCGTCAAGTGCAAAGAGGTTGCAGAAA
GAACTGGCTGATATTACTTTGGATCCTCCGCCAAACTGCAGTGCTGGGCCAAAAGGAGACAACTTGTACGAGTGGATGTC
AACCTTTTTGAGACCGCCTGGCTCTGTATATGAAGGTGGAATCTTTTTTTCTTGACATTCATTTCACCCAGGAGTATCCA
TTTAAGCCTCCCAAAGTTACTTTTCGTACTCGCATCTATCACTGTAATATCAACAGCCAGAGAGTAATTTGCTTAGATGT
GCTGAAAGATAATTGGAGTCCAGCACTAACAGTTTCAAAGGTCCTGCTATCGGTTTGCTCTTTACTTTCAGACTGCAACC
CAGCTGATCCGTTGGTTGCAAACATTGCCACTCAGTATTTCACCAACCACGAGGAGCATGACAGAATATCACGGCAGTGG
ACACAGAAATACGCCACG

ORF - retro_cint_33 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.74 %
Parental protein coverage: 98.01 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalSQQRATEESFSSEPNNETPG-PSSQVVEQKDETTEAKNNESAPSTQSPETKLVKHNLKNGSSDTSKSERE
SQQ.ATEE.F.SEPNNETPG.PSSQVVEQKD.TTEAKN.ESAPSTQ.PE.KLVKHNLK.GSSDTSKSERE
RetrocopySQQLATEERFISEPNNETPG<PSSQVVEQKDKTTEAKNEESAPSTQPPEIKLVKHNLKSGSSDTSKSERE
ParentalKKLKLDREKRAREMASASKVWLSKSPRGLSSSAKRLQKELADITLDPPPNCSAGPKGDNLYEWVSTILGP
KKLKLDREKR.RE.A.ASKVWLSKSPRGLSSSAKRLQKELADITLDPPPNCSAGPKGDNLYEW.ST.L.P
RetrocopyKKLKLDREKRPREIALASKVWLSKSPRGLSSSAKRLQKELADITLDPPPNCSAGPKGDNLYEWMSTFLRP
ParentalPGSVYEGGI-FFLDIHFTQEYPFKPPKVTFRTRIYHCNINSQGVICLDVLKDNWSPALTVSKVLLSVCSL
PGSVYEGGI.FFLDIHFTQEYPFKPPKVTFRTRIYHCNINSQ.VICLDVLKDNWSPALTVSKVLLSVCSL
RetrocopyPGSVYEGGI>FFLDIHFTQEYPFKPPKVTFRTRIYHCNINSQRVICLDVLKDNWSPALTVSKVLLSVCSL
ParentalLSDCNPADPLVANIATQYFTNREEHDRISRQWTQKYAT
LSDCNPADPLVANIATQYFTN.EEHDRISRQWTQKYAT
RetrocopyLSDCNPADPLVANIATQYFTNHEEHDRISRQWTQKYAT

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_33 retrocopy.

TSS - click to see more details

Ciona intestinalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_cint_33 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 42 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000035152 retrocopies
retro_amel_1117, retro_amel_483,
Canis familiaris ENSCAFG000000141633 retrocopies
retro_cfam_2076, retro_cfam_2161, retro_cfam_27,
Choloepus hoffmanni ENSCHOG000000073253 retrocopies
retro_chof_1756, retro_chof_2077, retro_chof_2358,
Choloepus hoffmanni ENSCHOG000000103412 retrocopies
retro_chof_1304, retro_chof_674,
Ciona intestinalis ENSCING00000006860 1 retrocopy
retro_cint_33 ,
Ciona intestinalis ENSCING000000187112 retrocopies
retro_cint_19, retro_cint_29,
Callithrix jacchus ENSCJAG000000115593 retrocopies
retro_cjac_3194, retro_cjac_3911, retro_cjac_3967,
Cavia porcellus ENSCPOG000000022512 retrocopies
retro_cpor_1036, retro_cpor_52,
Dasypus novemcinctus ENSDNOG000000054487 retrocopies
retro_dnov_1217, retro_dnov_1281, retro_dnov_1360, retro_dnov_156, retro_dnov_2026, retro_dnov_2508, retro_dnov_424,
Dipodomys ordii ENSDORG000000154411 retrocopy
retro_dord_785,
Equus caballus ENSECAG000000072331 retrocopy
retro_ecab_196,
Echinops telfairi ENSETEG000000193242 retrocopies
retro_etel_314, retro_etel_848,
Felis catus ENSFCAG000000077482 retrocopies
retro_fcat_1582, retro_fcat_913,
Felis catus ENSFCAG000000247191 retrocopy
retro_fcat_623,
Homo sapiens ENSG000001700351 retrocopy
retro_hsap_4653,
Gorilla gorilla ENSGGOG000000083931 retrocopy
retro_ggor_76,
Loxodonta africana ENSLAFG000000041501 retrocopy
retro_lafr_320,
Macropus eugenii ENSMEUG000000145171 retrocopy
retro_meug_2089,
Microcebus murinus ENSMICG000000167993 retrocopies
retro_mmur_1075, retro_mmur_15, retro_mmur_419,
Myotis lucifugus ENSMLUG000000251441 retrocopy
retro_mluc_712,
Macaca mulatta ENSMMUG000000080692 retrocopies
retro_mmul_1382, retro_mmul_1834,
Monodelphis domestica ENSMODG000000103012 retrocopies
retro_mdom_1679, retro_mdom_1688,
Mus musculus ENSMUSG000000217743 retrocopies
retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Mus musculus ENSMUSG000000270114 retrocopies
retro_mmus_2814, retro_mmus_3123, retro_mmus_3416, retro_mmus_3571,
Nomascus leucogenys ENSNLEG000000062901 retrocopy
retro_nleu_2068,
Oryctolagus cuniculus ENSOCUG000000060262 retrocopies
retro_ocun_134, retro_ocun_243,
Otolemur garnettii ENSOGAG000000075273 retrocopies
retro_ogar_2029, retro_ogar_2566, retro_ogar_626,
Otolemur garnettii ENSOGAG000000149564 retrocopies
retro_ogar_1343, retro_ogar_2512, retro_ogar_2682, retro_ogar_3443,
Ochotona princeps ENSOPRG000000106152 retrocopies
retro_opri_329, retro_opri_788,
Pongo abelii ENSPPYG000000129871 retrocopy
retro_pabe_3614,
Pan troglodytes ENSPTRG000000146931 retrocopy
retro_ptro_68,
Pteropus vampyrus ENSPVAG000000017731 retrocopy
retro_pvam_1451,
Rattus norvegicus ENSRNOG000000045441 retrocopy
retro_rnor_1236,
Rattus norvegicus ENSRNOG000000087943 retrocopies
retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii ENSSHAG000000014161 retrocopy
retro_shar_712,
Sus scrofa ENSSSCG000000112092 retrocopies
retro_sscr_759, retro_sscr_961,
Ictidomys tridecemlineatus ENSSTOG000000257992 retrocopies
retro_itri_1371, retro_itri_645,
Tupaia belangeri ENSTBEG000000099322 retrocopies
retro_tbel_1986, retro_tbel_3294,
Tarsius syrichta ENSTSYG000000022815 retrocopies
retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tursiops truncatus ENSTTRG000000013611 retrocopy
retro_ttru_1056,
Tursiops truncatus ENSTTRG000000051561 retrocopy
retro_ttru_1075,
Vicugna pacos ENSVPAG000000070073 retrocopies
retro_vpac_108, retro_vpac_315, retro_vpac_425,


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