RetrogeneDB ID: retro_csav_35

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_83:352166..353313(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000001602
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000003934
• Aliases: None
• Description: None

Sequence

>retro_csav_35
AAACCCAACATTGTATTCATCCTGGCCGACGACTTTGGCTTCAACGACATCGGGTACCATGCAGTGGAGCACCATTCTGA
TATGAAGACTCCATTTCTGGATTCCCTGGCAATGTCCGGAGTAAGGTTGGAGAATTATTACATTCAGCCGATTTGCTCTC
CATCTAGAAGTGTCTTAATGAGCGGAAGGTATCAGATCCACACTGGTTTGCAACATTACGTTATATCTCCCCAACAGAGG
AACGGGCTGCCTTTGGAAAACATTATACTGCCGGAGCAGTTGCATAAATGTGGCTACGATACTCACATGGTTGGGAAATG
GCATCTGGGATTCTACAAGGAAGACTTCACCCCTTGGAAACGTGGGTTCAATTCCTACTTTGGATATTTGACAGGTGGTG
GAAGATTATTACACAAAATGGAGATGTGATGGAAAATTGTGTGGTTACGATATGTCTTCAGAAAAGGGTCCAACTAATGA
GACTTATGGGAAGTATTCTGCTAACTTATTTGTTGACAAAGCGAAAGAGGCTATAGACAAAAGAAATACGAACCAACCTT
TATTTTTATACGTCGCTTTTCAGTCAGTTCATTCTCCAATGGAAGTTCCTGCATCTTATGAAAAACCGTTTGCTTATATT
AAAGATAACAACCGAAGAGCGTATGGTGGTATGGTGGCAGCCATGGATGAAGCTGTTAAAAACATCACACTTCACTTGCA
AGCTGCTGGAATATGGAACAACACACTTTTAATATTTTCAGCAGATAACGGTGGCCAGACACTGTCCGGTGGAAATAATT
ATCCTCTTAGAGGAAGGAAGCTTACACTTTGGGAAGGTGGGATCAAAGGTGTTGGATTCGTGCATGGGGAAATGCTTAAT
GTCCCAAACCCAAATGTTATAGTTAATAATGAAATGATGCATATTTCCGATTGGTTTCCCACAATAATGGCTGCAAGTCA
ATGCCCCTATGTAGAAGGCACACAAAAGCTTGACGGTGTTAATCAATGGGATACCATTCTTGGAAACGCTGTCTCACCCA
GAAAAGAAATTCTTCTAAACATAGACCCACTGTTCACGCCAATGTATTATAACCAAACTCCACGGAAATCTGTCAAAATG
GACTTTGATACGTCAGTTCACGCAGGA

Alignment

ORF - retro_csav_35 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.44 %
• Parental protein coverage: 75.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPHIVFVLADDFGYNDIGYHAREHCSQMYTPFLDSLAAKGVKLENYYVQPICSPTRGQLLTGRYQIHTGL
          .P.IVF.LADDFG.NDIGYHA.EH.S.M.TPFLDSLA..GV.LENYY.QPICSP.R..L..GRYQIHTGL
Retrocopy KPNIVFILADDFGFNDIGYHAVEHHSDMKTPFLDSLAMSGVRLENYYIQPICSPSRSVLMSGRYQIHTGL

Parental  AHGIIKAAQPYGLPLDNILLSQQLRKCGYKTNMVGKWHLGFFREEYLPWNRGFQNFFGFLNGG-VNHYTR
          .H..I...Q..GLPL.NI.L..QL.KCGY.T.MVGKWHLGF..E...PW.RGF...FG.L.GG....YT.
Retrocopy QHYVISPQQRNGLPLENIILPEQLHKCGYDTHMVGKWHLGFYKEDFTPWKRGFNSYFGYLTGG>EDYYTK

Parental  YHCEPKKTRRFCGYDMIDSRHGPINSTYGEYSTNLFVRKAKEMIDRHNKAKPMFLYLSLQAVHGPLQVPN
          ..C..K.....CGYDM..S..GP.N.TYG.YS.NLFV.KAKE.ID..N...P.FLY...Q.VH.P..VP.
Retrocopy WRCDGK----LCGYDM-SSEKGPTNETYGKYSANLFVDKAKEAIDKRNTNQPLFLYVAFQSVHSPMEVPA

Parental  QYLKRFKHIKDRNRKIYAGMVYAMDRGIRQLVKHLKRVRMWKDTIFIFSTDNGGQTTRGGNNWPLRGKKG
          .Y.K.F..IKD.NR..Y.GMV.AMD........HL.....W..T..IFS.DNGGQT..GGNN.PLRG.K.
Retrocopy SYEKPFAYIKDNNRRAYGGMVAAMDEAVKNITLHLQAAGIWNNTLLIFSADNGGQTLSGGNNYPLRGRKL

Parental  TLWEGGIRAVGFVHGKPLQLNGP--MVNHELLHVSDWYPTIMSATQCPLMVGTQNVDGYDQWDTIRKNKI
          TLWEGGI..VGFVHG..L....P...VN.E..H.SDW.PTIM.A.QCP...GTQ..DG..QWDTI..N..
Retrocopy TLWEGGIKGVGFVHGEMLNVPNPNVIVNNEMMHISDWFPTIMAASQCPYVEGTQKLDGVNQWDTILGNAV

Parental  SKRTEILHNIDPLHKKLTIGSEYREGFDVSVRAAIRSG
          S.R.EIL.NIDPL..........R.............G
Retrocopy SPRKEILLNIDPLFTPMYYNQTPRKSVKMDFDTSVHAG

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_35 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_35 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000003934	1 retrocopy	retro_csav_35 ,