RetrogeneDB ID: retro_csav_10

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_259:375263..376367(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000001550
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CSA.9185
• Ensembl ID: ENSCSAVG00000006503
• Aliases: None
• Description: None

Sequence

>retro_csav_10
TCTGAAAAAATGGGGATTTTAGAAAAAATATCTGAAATTGAGAAGGAAATTCAGCGAACACAGAAAAATAAAGCGACTGA
GTATCATCTTGGGCTGTTGAAGGCAAAACTCGCAAGATACAGAGCCCAACTATTGGAAGGTCCGAAAAGTTCAGGTCCAA
AAGGAGAGGGATTTGATGTCATGAAATCTGGAGACGCGAGAGTTGCGTTGGTTGGATTTCCATCTGTCGGGAAATCGACG
CTTCTGTCAACGCTCACGTCAACCGAGAGCGAATGTGCTTCGTATGAATTCACCACGTTGACCTGCATCCCCGGAGTTAT
CGAGCACAACGGAGCAAGAATCCAACTCCTTGATCTTCCAGGGATCATTGAAGGAGCTGCAGCGGGGAAGGGAAGAGGAA
GACAAGTGATCTCGGTCGCAAGAACCGCTGATATTGTTGTAATGATGCTCGATGCACTTAAGGGTGACGTGCAGAAAGAA
CTTCTGACAAAAGAACTCGAAGCAGTCGGAATTCGATTGAATAAAAAGCGACCGAACATTTATTTTAAGGAGAAGAAAGG
AGGTGGGATTTCTATTACTGCGACCTGCATCTTGACAAAAATCTCTGAGAGGATGATTAATTTAATCCTCCACGAATACA
AAATCTTCCACGCGGATGTAGTTTTCCGTGCTGATTATGGAACAGATGAATTTATTGATGTTGTGGTGGGCAAGCGGAAA
TACATGCCGTGTCTGTATGTTTACAACAAAATCGACCAGATTTCGATTGAGGAAGTTGATCGTATCGCATGGCAGCCTCA
TTGCGTCGTCATCAGCTGTAATATGCTGCTAAACCTTGATTACTTGAAAGATATGATATGGAAATATCTGCAATTAATCA
CAGTCTACACTAAAAAACCAGGGAAGAAGCCTGATTTTGCTGACGGTTTGATCCTGCGCTCGAACAGCAATGTAGAACAC
GCTTGCCATGCCATCCATAGAACACTGGTCGAGAATTTTAAATACGCGCAAGTATGGGGAAGAAGTGCTAAATATAATGG
TCAGCATGTGGGGTTGGGTCACAAACTTGCGCATGAGGATGTTGTCCTTGTTACGAAGAAATAA

Alignment

ORF - retro_csav_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.04 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSILTRISEIEAEMARTQKNKATAGHLGMLKARLAKLKRELITPKGGGGGGP-GEGFDVAKTGDARIGFV
          M.IL..ISEIE.E..RTQKNKAT..HLG.LKA.LA.....L....G....GP.GEGFDV.K.GDAR...V
Retrocopy MGILEKISEIEKEIQRTQKNKATEYHLGLLKAKLARYRAQLL--EGPKSSGPKGEGFDVMKSGDARVALV

Parental  GFPSVGKSTLLSNIAGVYSEVASYEFTTLTTVPGVIKYKGAKIQLLDLPGIIEGAKDGKGRGKQVIAVAR
          GFPSVGKSTLLS......SE.ASYEFTTLT..PGVI...GA.IQLLDLPGIIEGA..GKGRG.QVI.VAR
Retrocopy GFPSVGKSTLLSTLTSTESECASYEFTTLTCIPGVIEHNGARIQLLDLPGIIEGAAAGKGRGRQVISVAR

Parental  TCGLIFIVLDVLKPLGDKRLIEKELEGFGIRLNKKPPNIHYKVKEKGGINFQAMVPQSELDGELAKKILS
          T.......LD.LK....K.L..KELE..GIRLNKK.PNI..K.K..GGI...A..............IL.
Retrocopy TADIVVMMLDALKGDVQKELLTKELEAVGIRLNKKRPNIYFKEKKGGGISITATCILTKISERMINLILH

Parental  EYRIHNADIILKEDCSADDLIDMVEGNRVYIPCIYLLNKIDQISIEELDIIYKIPHCVPISAHHKWNFDD
          EY.I..AD.....D...D..ID.V.G.R.Y.PC.Y..NKIDQISIEE.D.I...PHCV.IS.....N.D.
Retrocopy EYKIFHADVVFRADYGTDEFIDVVVGKRKYMPCLYVYNKIDQISIEEVDRIAWQPHCVVISCNMLLNLDY

Parental  LLEKMWEYLKLIRIYTKPKGQLPDYEAPVVLSSEKSSVEDFCNKIHRTLLKQFKHALVWGSSVKYNPQSV
          L....W.YL.LI..YTK..G..PD......L.S..S.VE..C..IHRTL...FK.A.VWG.S.KYN.Q.V
Retrocopy LKDMIWKYLQLITVYTKKPGKKPDFADGLILRS-NSNVEHACHAIHRTLVENFKYAQVWGRSAKYNGQHV

Parental  GKEHVLMDEDVVQIVKR
          G..H.L..EDVV...K.
Retrocopy GLGHKLAHEDVVLVTKK

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

1 EST(s) were mapped to retro_csav_10 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BW512511	375234	375685	96.7	438	12	425

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_10 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007040	1 retrocopy	retro_amel_1448,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10 ,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,