RetrogeneDB ID: retro_csav_19

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_19:2141468..2142527(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CSA.10341
• Ensembl ID: ENSCSAVG00000001800
• Aliases: None
• Description: None

Sequence

>retro_csav_19
ATGGGTTGTGCTTCTTCGACGTCGGGCGATGCAATGGCAGCCAATAGATCCCGTCAGATCGACCGTGGCATCAAGGAAGA
TGCGAAACACGTCGACAAAGAAGTGAAATTGCTCCTGTTGGGTGCTGGAGAGTCGGGAAAGAGCACGATCGCGAAACAGA
TGAAGATTCTCTTCAAAGATGGCTTCTCGGAAAGAGAGAGGAACAGTTATAAACATGTTGTGTTTGCAAATGTCGTGCAA
TCGGTTGTCGCTATTGTGAAGGCGATGCCAACTCTACAGATCGAATTCGAGAACCCCGATCGTTTGGAAGACGCTAAAAA
AGTACTGACTGCCGGCCAGACGTTGGGAGATTTTGAGCTAGCTGGTGAGATCGGAGAAGCGGCGATACGACTATGGGAGG
ATGCAGGACTCCGCAAGAGTTACGTGCGTTCGCGCGAGTACCAGCTTAACGACTCGGCGGAGTACTATCTCCAAGCGCTG
GAGCGATTGAGCGACCCTGGCTACATCCCTACTGAGCAAGATGTCCTGAGGACTCGAGTTAAAACAACCGGTATCACTGA
GACGAACTTCAATTACAAAAATCTTGAATTCCGGCTGATTGATGTCGGAGGACAGAGATCAGAGCGGAAGAAGTGGATTC
ATTGTTTTGAGGATGTAACAGCTATTATTTTCTGCGTCGCGCTCTCGGCGTACGATCTTCTGTTGGCGGAAGACGAAGAA
ACAAACAGGATGCACGAGAGCATGCGACTCTTCGACTCGATATGCAACAACGCTTGGTTCAGGAACACATCGATGATCCT
CTTTTTGAACAAAACCGACATCTTCCGGAGCAAGATCGAACACTCTCCGCTGAGCGCTTGCTTCCCGGATTACAAGGGGA
AGAACACCTTCGACCAGGCAGCGCCTTACATTCAGATTCAGTTCGAAAATCTGAACCATCACCCTGAAAAAATGGTGTAC
ACCCACTTTACATGCGCGACGGACACTACGAATGTGCAGTTCGTGTTTGATGCGGTTTCCGACGTCATTTTAACCAAGGT
GCTCGGGGATTTGGGTCTG

Alignment

ORF - retro_csav_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.71 %
• Parental protein coverage: 99.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGCTVSTD-DKAANERSRAIDRNLRVDGDKQSREVKLLLLGAGESGKSTIVKQMKIIHEDGYSEEECLQY
          MGC..ST..D..A..RSR.IDR....D......EVKLLLLGAGESGKSTI.KQMKI...DG.SE.E...Y
Retrocopy MGCASSTSGDAMAANRSRQIDRGIKEDAKHVDKEVKLLLLGAGESGKSTIAKQMKILFKDGFSERERNSY

Parental  KAVVYSNTLQSLITIVRAMGNLKIDFGSPERADDARQLFSLAGSLDDGEMTQELGDCMKRMWSDKGVQVC
          K.VV..N..QS...IV.AM..L.I.F..P.R..DA.........L.D.E...E.G....R.W.D.G....
Retrocopy KHVVFANVVQSVVAIVKAMPTLQIEFENPDRLEDAKKVLTAGQTLGDFELAGEIGEAAIRLWEDAGLRKS

Parental  FSRSREFQLNDSAQYYLDALERLTEHHYVPTQQDVLRTRVKTTGIVEVHFNFKGLTFKMFDVGGQRSERK
          ..RSRE.QLNDSA.YYL.ALERL....Y.PT.QDVLRTRVKTTGI.E..FN.K.L.F...DVGGQRSERK
Retrocopy YVRSREYQLNDSAEYYLQALERLSDPGYIPTEQDVLRTRVKTTGITETNFNYKNLEFRLIDVGGQRSERK

Parental  KWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHESMKLFDSICNNKWFTETSIILFLNKKDLFEVKIL
          KWIHCFE.VTAIIFCVALSAYDL.LAEDEE.NRMHESM.LFDSICNN.WF..TS.ILFLNK.D.F..KI.
Retrocopy KWIHCFEDVTAIIFCVALSAYDLLLAEDEETNRMHESMRLFDSICNNAWFRNTSMILFLNKTDIFRSKIE

Parental  KSPLTICFPEYPGQNTYEEAAAYIQLQFEDLNKRKDSKEIYTHFTCATDTTNIQFVFDAVTDVIIKNNLK
          .SPL..CFP.Y.G.NT...AA.YIQ.QFE.LN.....K..YTHFTCATDTTN.QFVFDAV.DVI....L.
Retrocopy HSPLSACFPDYKGKNTFDQAAPYIQIQFENLNHHPE-KMVYTHFTCATDTTNVQFVFDAVSDVILTKVLG

Parental  DCGL
          D.GL
Retrocopy DLGL

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_19 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_19 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.

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010970	1 retrocopy	retro_acar_40,
Choloepus hoffmanni	ENSCHOG00000012718	1 retrocopy	retro_chof_359,
Ciona intestinalis	ENSCING00000005305	1 retrocopy	retro_cint_14,
Callithrix jacchus	ENSCJAG00000004925	1 retrocopy	retro_cjac_1091,
Ciona savignyi	ENSCSAVG00000001800	1 retrocopy	retro_csav_19 ,
Danio rerio	ENSDARG00000021647	1 retrocopy	retro_drer_19,
Felis catus	ENSFCAG00000007008	1 retrocopy	retro_fcat_157,
Microcebus murinus	ENSMICG00000011752	1 retrocopy	retro_mmur_1103,
Otolemur garnettii	ENSOGAG00000012525	1 retrocopy	retro_ogar_1470,
Otolemur garnettii	ENSOGAG00000013587	1 retrocopy	retro_ogar_993,
Rattus norvegicus	ENSRNOG00000016592	1 retrocopy	retro_rnor_505,
Tupaia belangeri	ENSTBEG00000015771	1 retrocopy	retro_tbel_2449,
Tarsius syrichta	ENSTSYG00000000556	1 retrocopy	retro_tsyr_288,