RetrogeneDB ID: retro_csav_9

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_77:3224224..3224974(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000008605
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CSA.5346
• Ensembl ID: ENSCSAVG00000011723
• Aliases: None
• Description: None

Sequence

>retro_csav_9
GTTTCAAATATTGTAATAAAAATGACTCAATCTAAAGAAGAGCTTGTTGCCAGCGCCCGGCTTGCCGAGCAAGCGGAGAG
GTATGAAGACATGGTAGCTGAAATGAAGAAATTTCTGGAGTTGGACGCAAACTTAACAACGGAAGAACGGAACCTACTTT
CAGTTGCATTTAAAAACGTGATCGGCGCTCGCAGGTCTTCGTGGAGAATTATCAATAGTATCGAGCAGAAGGATAAAGAC
AAGGGAAAGCCGACCGATATTGTTGAAGCCTACAGGGAAAAAATAGAGTCGGAGTTGCAAACCTGGTGCCAGGAAGTGAT
TCAACTTCTGGAAACGAAACTGATCCCGGCATGCAACACTGCCTCCGATCAGCACGAGGCTTCAGTCTTCTACAGAAAAA
TGAAGGGCGATTACTACAGGTACATGGCAGAGTTCATTGAAAACAAGGAGGATGTCGTTAAATCAAGTCTGGATGCGTAC
GACGAGGCGAAAGACGTTTCAGAGGCACATCTGAAACCAACGAATCCTATACGTCTTGGGCTGGCGCTGAACTTCTCTGT
CTTTTACTATGAGATCAAAGGCGATCAAACAAAAAGGGCGTGCGAGCTCGCCAAGACTGCCTTCGACGCTGCGATTGCTG
AACTGGACCAGCTACCAGAAGATTCGTACAAAGACTCGACCCTGATCATGCAGCTCCTTCGTGACAACCTCACCCTTTGG
ACGTCGGACGCATCTGGGGACCAGGAAGAG

Alignment

ORF - retro_csav_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.61 %
• Parental protein coverage: 94.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDKREDIVYRAKLAEQAERYDEMVAEMKSVAKLGVELSVEERNLLSVAFKNVIGARRASWRIISSIEQKE
          ....E..V..A.LAEQAERY..MVAEMK....L...L..EERNLLSVAFKNVIGARR.SWRII.SIEQK.
Retrocopy TQSKEELVASARLAEQAERYEDMVAEMKKFLELDANLTTEERNLLSVAFKNVIGARRSSWRIINSIEQKD

Parental  E---KNNEMISAYKKKVEDELKKICTDILDLIKTFLIPNSVNAESK----VFYFKMQGDYHRYLAEFETG
          ....K......AY..K.E.EL...C.....L..T.LIP....A.......VFY.KM.GDY.RY.AEF...
Retrocopy KDKGKPTDIVEAYREKIESELQTWCQEVIQLLETKLIPACNTASDQHEASVFYRKMKGDYYRYMAEFI--

Parental  SDRKDAAEKSLVSYKGAEEVAQTELAPTHPIRLGLALNFSVFYYEIL-NSPDRACRLAKTAFDDAIAELD
          ....D....SL..Y..A..V....L.PT.PIRLGLALNFSVFYYEI......RAC.LAKTAFD.AIAELD
Retrocopy ENKEDVVKSSLDAYDEAKDVSEAHLKPTNPIRLGLALNFSVFYYEIKGDQTKRACELAKTAFDAAIAELD

Parental  TLSEESYKDSTLIMQLLRDNLTLWTSDMQGETEE
          .L.E.SYKDSTLIMQLLRDNLTLWTSD..G..EE
Retrocopy QLPEDSYKDSTLIMQLLRDNLTLWTSDASGDQEE

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_9 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_9 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 19 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005664	3 retrocopies	retro_btau_1485, retro_btau_372, retro_btau_954,
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Cavia porcellus	ENSCPOG00000008007	1 retrocopy	retro_cpor_307,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9 ,
Dasypus novemcinctus	ENSDNOG00000003808	2 retrocopies	retro_dnov_1452, retro_dnov_2602,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Felis catus	ENSFCAG00000011368	1 retrocopy	retro_fcat_1636,
Homo sapiens	ENSG00000108953	4 retrocopies	retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
Macropus eugenii	ENSMEUG00000015460	12 retrocopies	retro_meug_1290, retro_meug_1396, retro_meug_1536, retro_meug_16, retro_meug_1926, retro_meug_196, retro_meug_2153, retro_meug_2163, retro_meug_835, retro_meug_9, retro_meug_982, retro_meug_986,
Monodelphis domestica	ENSMODG00000010174	2 retrocopies	retro_mdom_1567, retro_mdom_744,
Nomascus leucogenys	ENSNLEG00000000656	2 retrocopies	retro_nleu_2067, retro_nleu_2868,
Oryctolagus cuniculus	ENSOCUG00000014607	2 retrocopies	retro_ocun_1062, retro_ocun_1576,
Otolemur garnettii	ENSOGAG00000006155	2 retrocopies	retro_ogar_1003, retro_ogar_2144,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,
Pan troglodytes	ENSPTRG00000008521	5 retrocopies	retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Ictidomys tridecemlineatus	ENSSTOG00000005084	1 retrocopy	retro_itri_1175,
Vicugna pacos	ENSVPAG00000010288	3 retrocopies	retro_vpac_230, retro_vpac_411, retro_vpac_559,