RetrogeneDB ID: retro_csav_1

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_30:3357785..3359282(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000010355
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CSA.8408
• Ensembl ID: ENSCSAVG00000004455
• Aliases: None
• Description: None

Sequence

>retro_csav_1
ACAATAAGGTCATTTTTCTATTATACATTTATAAACAAAGAAATGTCAGAAAATGATGAACCAAGCACTTCATTTCAAGA
TGTTACAAAAACTCAGCAATCAGTTAACCTGAAGCAGAAGATAACACTGGCAAATGGCGTGGCACTTATTGTTGGAAACA
TCATTGGCTCTGGTATTTTTCTAAGTCCAAAAGGAGTCCAGGAAAAATGCGGCTCACCTGGTTTAAGTTTAATAATCTGG
TCAATATGTGGAGTCTTTTCTCTAATCGGTGCTTTGTGCTATGCTGAACTTGGTACAACTATTATTAAATCCGGTGCCAG
TTATGCCTACATTTTACGAGCCTTTGGCCCTTTAGTAGGTTTTGTTCGACTGTGGATATCTGTTCTTATTATTGAGCCTA
CAGTCCAAGCAGCTATTGCTATAACGTTTGCGAATTATTTAATTCAACCGTTTTTCCCCACATGTGAACCACCATTTTAT
GCTGTACGTTTGTTAGCAGCTGCTTGTGTTATCATAATCATGGTAATGAATTGCTTCAGTGTACGGTATGGAACAAGAAT
ACAAGACATCTTTGCTTATGCCAAAGTCCTTGCCCTGATTGTCATTATGATTGTTGGGTTTATTGCACTTGGCAATGGAA
CATCTTCCAGTTCATTGGCTGAACCTTGGAAAGGAACAACTAATAATATTGGAAACATAGCCCTTGCGTTATACTCTGGC
CTGTATGCCTATTCGGGATGGGATACACTGAACTTCATGGTGGAAGAGTTGCAGGATCCATATCGCAATCTACCGAAGGC
AATTTATATTTCACTTCCACTCTGTACTATCATTTACATTCTAACAAACATTGCTTACTATGCTATTTTGACACCGGCTG
AATTGATAGCAACGGATGCTGTTGCTGTCAGCTTTGCTGGTAAAACATTAGGAGTCATGCAGTGGACCATACCCATTGCT
GTAGCAATGTCAACTTTTGGTGGACTGAATTCATCTATCATGGCCTCTTCCCGTTTGTTTTTCGTCGGTGCACGTGAAGG
TCATTTACCGGACTACCTTGCCATGGTTAATTTTAAAAGATTCACCCCTGCTCCAAGTTTGCTTTTCACCGGGACACTTA
CTCTTGTATTCCTATGTGTAAGTGATGTTTTTGACCTGATTAACTACTACAGCTTCATGTATTGGCTAGCAGTTGGTTTA
TCAATTGCTGGGCAAATCTACCTTAGATTTACCGAACCCAAACTGCCCAGACCTCTAAAAGTTAATATTATTTTCCCCAT
AATATTTTGTCTTGCCTGCTTGTTTTTGGTTATTGTGCCATTCTTTGAAGAAACACGGGATTCACTAATCGGTACTGCCA
TTCTTGCAACTGGTATACCAATCTACTTTTTCTTCGTTTACTTGAAACAGCCAGCATTCCTCTCAAAGATTAGCAACGCA
GTAACCGGATTTCTACAAAAGTTGCTTCCTGTTTCTATCTCAGATATGGAAATTGAG

Alignment

ORF - retro_csav_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.15 %
• Parental protein coverage: 95.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGEESSSSDSSEGVGESKIILKQRITLVNACALIVGTIIGSGIFISPVGVFREVNSVGLSLIVWTIGGFF
          ...E.S.S............LKQ.ITL.N..ALIVG.IIGSGIF.SP.GV.....S.GLSLI.W.I.G.F
Retrocopy ENDEPSTSFQDVTKTQQSVNLKQKITLANGVALIVGNIIGSGIFLSPKGVQEKCGSPGLSLIIWSICGVF

Parental  STIGALCYAELGTTIVKSGGDYAYIREFYGPLPAFLRLWIALLIIRPTSQAAIALTFSSYLVQPFFPNCT
          S.IGALCYAELGTTI.KSG..YAYI....GPL..F.RLWI..LII.PT.QAAIA.TF..YL.QPFFP.C.
Retrocopy SLIGALCYAELGTTIIKSGASYAYILRAFGPLVGFVRLWISVLIIEPTVQAAIAITFANYLIQPFFPTCE

Parental  ELMPESSIRLFAALSLIILSLVNCMSVRWATRVQDVFTAAKLLALAIIIIIGVVKIGQATHTHTHTS-FK
          ...P....RL.AA...II....NC.SVR..TR.QD.F..AK.LAL..I.I.G....G..T.........K
Retrocopy P--PFYAVRLLAAACVIIIMVMNCFSVRYGTRIQDIFAYAKVLALIVIMIVGFIALGNGTSSSSLAEPWK

Parental  GTTSDIGRIVIAFYNSLYAYGGWNYLNFVTEEMKDPYKNLPRAIMISLPLVSFIYVTANIAYFTVLSPTE
          GTT..IG.I..A.Y..LYAY.GW..LNF..EE..DPY.NLP.AI.ISLPL...IY...NIAY...L.P.E
Retrocopy GTTNNIGNIALALYSGLYAYSGWDTLNFMVEELQDPYRNLPKAIYISLPLCTIIYILTNIAYYAILTPAE

Parental  FGISNAVAVLFGDKVLGVMSWIIPVFVSLSCFGSVNGSIFTSSRLFFVGAREGQLPNILAMIHTKHFTPV
          .....AVAV.F..K.LGVM.W.IP..V..S.FG..N.SI..SSRLFFVGAREG.LP..LAM...K.FTP.
Retrocopy LIATDAVAVSFAGKTLGVMQWTIPIAVAMSTFGGLNSSIMASSRLFFVGAREGHLPDYLAMVNFKRFTPA

Parental  PAIMFNCILSLLYLVSGDIWSLITYFSFFNWLCVGMAILGLLHWRYKYPDMERPVKMHISLPITFFIAAA
          P...F...L.L..L...D...LI.Y.SF..WL.VG..I.G....R...P...RP.K..I..PI.F..A..
Retrocopy PSLLFTGTLTLVFLCVSDVFDLINYYSFMYWLAVGLSIAGQIYLRFTEPKLPRPLKVNIIFPIIFCLACL

Parental  FLVVMAVYAAPKECLIGACIVLTGIPVYLIGVRYQHKQPKWLDNGMDSVTIFCQTFLGV
          FLV...........LIG..I..TGIP.Y...V....KQP..L......VT.F.Q..L.V
Retrocopy FLVIVPFFEETRDSLIGTAILATGIPIYFFFVYL--KQPAFLSKISNAVTGFLQKLLPV

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

5 EST(s) were mapped to retro_csav_1 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BW523458	3357798	3358280	98.8	476	6	470
BW524314	3357805	3358342	98.4	527	8	516
BW532864	3357789	3358167	96.9	368	9	357
BW538884	3357692	3358324	96.3	594	21	568
BW571721	3357789	3358396	97.4	594	13	580

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_1 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000004455	1 retrocopy	retro_csav_1 ,
Ictidomys tridecemlineatus	ENSSTOG00000025706	1 retrocopy	retro_itri_1891,