RetrogeneDB ID: retro_cint_28

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 8:2308004..2308859(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000005532
• Aliases: None
• Description: None

Sequence

>retro_cint_28
ATTATCAAACCCGATCAGTATGGCGTCGGGGATTTACTGCATATGAGGTCGCCTAGAAATTACTTGCTTGGAAAGGACAG
AGAGCGTGGTGTTCTCGCTACAGTCCGACAGCAGTTGAAAAAAGCGAATTACCACAACTTTAGTGATCTCAGGACAGCGT
TCGAGCATTACGATACAGACAAAGTCGGATGGCTCGACGCCCAAAAGATCCGGGACGCTTGTTGGAAGTTTAACTTGCCA
ATTGATAATGACTTGCTCGCATCTCTTATGCATTACTGCAAAGTTGAAACCGACGACGAAAAAGACTGCAAACTTGATTA
CATCAATTTTGTCAACTTTCTCAACTGGAAGGATAAATACGCAGTCTCTAGGCATGATAGCGGGCCAGTTTCACCAGTCA
AAGACATAGACGTACCAAAACTATGCAAGCAGATTGACGATGCTATGACAAACCATTTAACGTCTTCTTCAACAATTGAT
GCTGTGGCCGGAAAAGTTAACACAAACGAATTCCGGACCTACGGTGTGCCCACTGTGCGATCTGACCTGCCTGCGCCACG
CACACGGCGCATAAGCGACCATAAGAACTATGGCGACGAGTCGGACGCTTACGGGCTTGTCAATCCATCATTGTATACTC
GACGAGGCGTTTATGAAAGGGACTTTTTCGAACCGCGTAAGCGTGAAGATATTAGGGCTATTTTCGATGCGATTGAAATC
CAGCTTTCGGAAGAGGTGTTTGACAAGATTTGGAAACTTGCTGTGCAATGGAACTGCTGTTCTTCTGAAGGGAAAGAATT
AGCGTCTGTGGAAGCTTTCCGCAAAGTGCTGGACAAATTAAGAGCGTCATCTTTA

Alignment

ORF - retro_cint_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.17 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRPDEYGAGDLLHGRSPDAYLRGRDRERGVLHAIRQHLKKANYHNFNNLAQAFAHYDRNQDGFIDGEEL
          ...PD.YG.GDLLH.RSP..YL.G.DRERGVL...RQ.LKKANYHNF..L..AF.HYD....G..D....
Retrocopy IIKPDQYGVGDLLHMRSPRNYLLGKDRERGVLATVRQQLKKANYHNFSDLRTAFEHYDTDKVGWLDAQKI

Parental  RNVCYQLNVPVEDEMLFLLMSYCCAESTDKEHEAKIDYVKFANFLNWKDKMPMSADKKTGKELPIP--DT
          R..C...N.P.....L..LM.YC..E.TD.E...K.DY..F.NFLNWKDK...S.....G...P....D.
Retrocopy RDACWKFNLPIDNDLLASLMHYCKVE-TDDEKDCKLDYINFVNFLNWKDKYAVSR-HDSGPVSPVKDIDV

Parental  PTIQKQIDRAVTQHKTSSSVIGALSA-VDASQYRKYGIPTVRSDIAPPKLRRVSDHVNYGDESDAYGLVN
          P...KQID.A.T.H.TSSS.I.A....V.....R.YG.PTVRSD...P..RR.SDH.NYGDESDAYGLVN
Retrocopy PKLCKQIDDAMTNHLTSSSTIDAVAGKVNTNEFRTYGVPTVRSDLPAPRTRRISDHKNYGDESDAYGLVN

Parental  PTMYSEKGIYEQDMFEARPKTEIESIFTNIGVNMTPEMFNELWELAKQRD---PRGRNLVSVETFRSVLD
          P..Y...G.YE.D.FE.R....I..IF..I......E.F...W.LA.Q.......G..L.SVE.FR.VLD
Retrocopy PSLYTRRGVYERDFFEPRKREDIRAIFDAIEIQLSEEVFDKIWKLAVQWNCCSSEGKELASVEAFRKVLD

Parental  DVQATSI
          ...A.S.
Retrocopy KLRASSL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ciona intestinalis was not studied using RNA-Seq expression data.

ChIP-Seq

Ciona intestinalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cint_28 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_28 was not experimentally validated.

Homology

Retrocopy orthology:

Ciona intestinalis 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 intestinalis	ENSCING00000005532	1 retrocopy	retro_cint_28 ,