RetrogeneDB ID: retro_cint_21

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 8:774547..775210(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000021593
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000003959
• Aliases: None
• Description: None

Sequence

>retro_cint_21
ATGGCAAACTCCAATGCAGTCCAACAGCAGCAAAAAGATGCGGCAGATCAAAATTTTGACTACATGTTTAAGTTGTTAAT
TATTGGTAACAGCAGTGTTGGGAAAACCTCCTTTCTGTTTCGATATGCTGATGATTCATTTACAAGTGCATTTGTCTCCA
CGGTGGGGATTGACTTCAAAGTGAAAACAGTATTTCGGCAAGACAAACGAGTGAAACTGCAAATATGGGACACCGCTGGA
CAAGAGCGTTACAGGACAATTACTACAGCTTATTACAGAGGGGCGATGGGCTTTATCTTAATGTATGACATCACAAATGA
AGAATCTTTTAACAGTGTTCAAGATTGGTCAACCCAGATTAAAACGTATTCTTGGGATAATGCTCAAGTAACGTTGGTTG
GCAACAAATGTGACATGGAGGACGAAAGAGTGATTTCAACTGAACGAGGAAAGCAACTTGCTGATCAACTTGGATTTGAG
TTTTTCGAAACTAGTGCAAAAGATAATGTAAATGTGAAGCAAGTGTTCGAACGTCTGGTGGACCTCATTTGTGTGAAGAT
GTCTGAAAGCCTGGAATCTGATCCTTCACTAGGAAATGCCAACAAAGGCACACGTCTGACTGAAAATGATCAAGATCAAG
CTGCTGGGAACTGCGCTTGTTGA

Alignment

ORF - retro_cint_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.94 %
• Parental protein coverage: 80.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKKTYDLLFKLLLIGDSGVGKTCVLFRFSDDAFNTTFISTIGIDFKIKTVELNGKKIKLQIWDTAGQERF
          A....D..FKLL.IG.S.VGKT..LFR..DD.F...F.ST.GIDFK.KTV....K..KLQIWDTAGQER.
Retrocopy ADQNFDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRQDKRVKLQIWDTAGQERY

Parental  HTITTSYYRGANGIMLVYDITNTKSFENISKWLRNIEEHASEDVEKMLLGNKCDMEDKRMISKERGEMIA
          .TITT.YYRGA.G..L.YDITN..SF.....W...I...........L.GNKCDMED.R.IS.ERG...A
Retrocopy RTITTAYYRGAMGFILMYDITNEESFNSVQDWSTQIKTYSWDNAQVTLVGNKCDMEDERVISTERGKQLA

Parental  KEHGIKFYETSAKNNINIETAF
          ...G..F.ETSAK.N.N....F
Retrocopy DQLGFEFFETSAKDNVNVKQVF

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_21 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_21 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000003959	1 retrocopy	retro_cint_21 ,
Echinops telfairi	ENSETEG00000010795	1 retrocopy	retro_etel_661,
Myotis lucifugus	ENSMLUG00000009937	1 retrocopy	retro_mluc_2453,
Monodelphis domestica	ENSMODG00000015821	1 retrocopy	retro_mdom_1577,
Tupaia belangeri	ENSTBEG00000016698	1 retrocopy	retro_tbel_4738,