RetrogeneDB ID: retro_csav_6

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_37:644056..644671(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000002881
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CSA.4391
• Ensembl ID: ENSCSAVG00000001209
• Aliases: None
• Description: None

Sequence

>retro_csav_6
TCATATGAAAGTCATCTTCTCCAGTCCACCAAAGCCCAGATCTCAAAACCCGCTCCAAAATGGGAGGGCACTGCCATTGT
AGAGGGTGAAATTAAAACCATTAAGCTGACTGATTACTTGGGAAAATACCTAGTGTTCTTCTTTTACCCTCTTGATTTCA
CCTTTGTATGCCCGACAGAAATCATTGCGTTCTCGGACCGGATTGAGGAGTTTAGAAAAATGAATGTTGAAGTTGTTGCC
GCTTCAGTTGACTCTCACTTCACACATCTCGCATGGCTTAACACTCGCCGCTCCGAAGGTGGTCTTGGAAAGCTGAATAT
TCCCCTTCTCTCCGATCTCACCCATAAAATCTCTCGAGATTACGGAGTCCTCTTGGAGGACCTCGGACACACTCTCCGTG
GACTCTTCATCATCGACCCAAAAGGAGTCCTCCGTCAAATCACGATGAACGATCTTCCCGTCGGTAGGTCCGTGGACGAA
ACCATTAGATTGGTCCAAGCGTTCCAACACACTGATGAACACGGTGAGGTTTGCCCCGCTGGATGGGAGCCCGGCAAAGA
TACCATCATCCCAGACCCTAAGGACAAGCTCAAGTACTTCAGCAAAACTTCAAAG

Alignment

ORF - retro_csav_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.73 %
• Parental protein coverage: 90.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASVTQPAPDFKGTSVINGEFKEICLKDYLGKYLVLFFYPLDFTFVCPTEIISFSERSGEFEKCDTSVVGV
          A....PAP...GT....GE.K.I.L.DYLGKYLV.FFYPLDFTFVCPTEII.FS.R..EF.K....VV..
Retrocopy AQISKPAPKWEGTAIVEGEIKTIKLTDYLGKYLVFFFYPLDFTFVCPTEIIAFSDRIEEFRKMNVEVVAA

Parental  SVDSHFSHLAWINTPRKEGGLGPMKIPLLSDLTKSVSKDYGVLLEKAGIALRGLFIIDDKGTIWHASVND
          SVDSHF.HLAW.NT.R.EGGLG...IPLLSDLT...S.DYGVLLE..G..LRGLFIID.KG.......ND
Retrocopy SVDSHFTHLAWLNTRRSEGGLGKLNIPLLSDLTHKISRDYGVLLEDLGHTLRGLFIIDPKGVLRQITMND

Parental  LPVGRSVDEVLRLVQAFQFVDKHGEVCPASWTPGSKTIKPSIEGSKKYFESSN
          LPVGRSVDE..RLVQAFQ..D.HGEVCPA.W.PG..TI.P......KYF....
Retrocopy LPVGRSVDETIRLVQAFQHTDEHGEVCPAGWEPGKDTIIPDPKDKLKYFSKTS

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Ciona savignyi was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_csav_6 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_6 was not experimentally validated.

Homology

Retrocopy orthology:

Ciona savignyi 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.

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008731	1 retrocopy	retro_btau_562,
Canis familiaris	ENSCAFG00000012109	3 retrocopies	retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Callithrix jacchus	ENSCJAG00000019636	3 retrocopies	retro_cjac_1333, retro_cjac_3082, retro_cjac_653,
Ciona savignyi	ENSCSAVG00000001209	1 retrocopy	retro_csav_6 ,
Dasypus novemcinctus	ENSDNOG00000001359	3 retrocopies	retro_dnov_1052, retro_dnov_2373, retro_dnov_745,
Equus caballus	ENSECAG00000017026	1 retrocopy	retro_ecab_408,
Erinaceus europaeus	ENSEEUG00000009299	1 retrocopy	retro_eeur_238,
Homo sapiens	ENSG00000165672	3 retrocopies	retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla	ENSGGOG00000026364	1 retrocopy	retro_ggor_986,
Macropus eugenii	ENSMEUG00000007732	3 retrocopies	retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus	ENSMICG00000007627	1 retrocopy	retro_mmur_475,
Myotis lucifugus	ENSMLUG00000012871	3 retrocopies	retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta	ENSMMUG00000008294	2 retrocopies	retro_mmul_1307, retro_mmul_1517,
Monodelphis domestica	ENSMODG00000009286	1 retrocopy	retro_mdom_1062,
Mustela putorius furo	ENSMPUG00000003074	1 retrocopy	retro_mputfur_1032,
Mus musculus	ENSMUSG00000024997	1 retrocopy	retro_mmus_2443,
Nomascus leucogenys	ENSNLEG00000016698	3 retrocopies	retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus	ENSOCUG00000017334	2 retrocopies	retro_ocun_135, retro_ocun_1434,
Pongo abelii	ENSPPYG00000002700	1 retrocopy	retro_pabe_1906,
Pan troglodytes	ENSPTRG00000002992	1 retrocopy	retro_ptro_29,
Ictidomys tridecemlineatus	ENSSTOG00000002537	2 retrocopies	retro_itri_1098, retro_itri_1753,
Tupaia belangeri	ENSTBEG00000011064	5 retrocopies	retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus	ENSTTRG00000010878	2 retrocopies	retro_ttru_1703, retro_ttru_881,