RetrogeneDB ID: retro_csav_4

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_207:137123..137633(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000001501
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000009498
• Aliases: None
• Description: None

Sequence

>retro_csav_4
ATGGTTGGCTCGGCGTTAAAACGGCTGATGGCTGAATACAAGCAATTATCACTGAACCCACCAGAAGGAATCGTTGCTGG
ACCTATCAATGAGGAAAACTTCTTCGAATGGGAAGCTATGATACTCGGCCCTGAAGACACCCCTTTTGAGGGTGGGGTTT
TTCGTACGACGCTCAATTTCCCTACAGATTACCCAATGAGCCCGCCGAAAATGAAATTTGTTTCCGAAATGTTTCACCCT
AACATCTACCCCGACGGACGGGTTTGTATATCAATACTCCATTCACCAGGAGATGACCCGATGGGATATGAAACGAGCGC
TGAACGCTGGTCTCCCGTCCAAAGTATTGAAAAGATCCTTCTCTCTGTGATGAGCATGCTTGCAGAACCGAACCCAGAAT
CCGGCGCGAACGTAGACGCCTCGAAAATGTGGCGAGATAATCAGGAACAATTCATCAAACATGCAGAGAAACTTGTTCGA
AAGTCGCTAGATTTACCAGAGAATTTATAA

Alignment

ORF - retro_csav_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.7 %
• Parental protein coverage: 98.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELQKNPVDGFSAGLVDENNIYKWEVLIIGPVDSLYEGGYFKAHLTFPEEYPQRPPKLKFISEMWHPNVGK
          .L..NP..G..AG...E.N...WE..I.GP.D...EGG.F...L.FP..YP..PPK.KF.SEM.HPN...
Retrocopy QLSLNPPEGIVAGPINEENFFEWEAMILGPEDTPFEGGVFRTTLNFPTDYPMSPPKMKFVSEMFHPNIYP

Parental  DGFVCISILHEPGDDKFGYEKAAERWLPVHTVETIMVSTISMLCDPNDESPANVDAAKQFREDKHKFKKQ
          DG.VCISILH.PGDD..GYE..AERW.PV...E.I..S..SML..PN.ES.ANVDA.K..R.....F.K.
Retrocopy DGRVCISILHSPGDDPMGYETSAERWSPVQSIEKILLSVMSMLAEPNPESGANVDASKMWRDNQEQFIKH

Parental  VARCVRLS
          ....VR.S
Retrocopy AEKLVRKS

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_4 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_4 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014433	1 retrocopy	retro_btau_604,
Choloepus hoffmanni	ENSCHOG00000011801	1 retrocopy	retro_chof_2181,
Ciona savignyi	ENSCSAVG00000009498	1 retrocopy	retro_csav_4 ,
Macropus eugenii	ENSMEUG00000009769	3 retrocopies	retro_meug_360, retro_meug_473, retro_meug_647,
Myotis lucifugus	ENSMLUG00000002118	1 retrocopy	retro_mluc_104,
Oryctolagus cuniculus	ENSOCUG00000000248	1 retrocopy	retro_ocun_152,
Otolemur garnettii	ENSOGAG00000008795	1 retrocopy	retro_ogar_2554,
Rattus norvegicus	ENSRNOG00000010041	3 retrocopies	retro_rnor_2496, retro_rnor_317, retro_rnor_970,
Sarcophilus harrisii	ENSSHAG00000002399	1 retrocopy	retro_shar_75,
Tupaia belangeri	ENSTBEG00000006117	1 retrocopy	retro_tbel_2852,
Tetraodon nigroviridis	ENSTNIG00000008566	1 retrocopy	retro_tnig_11,
Takifugu rubripes	ENSTRUG00000005995	1 retrocopy	retro_trub_4,
Tursiops truncatus	ENSTTRG00000000595	1 retrocopy	retro_ttru_1578,
Drosophila melanogaster	FBgn0058045	1 retrocopy	retro_dmel_6,