RetrogeneDB ID: retro_cint_6

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 9:2743213..2744056(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000004219
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000000485
• Aliases: None
• Description: None

Sequence

>retro_cint_6
AGAATACCCCAGGTAGAAATGCAACAAAGGGCTGAACAAAATGCTCGATTTGACCAGAATAAAGCAGGAGGTGCGGGAAT
ATGTGGTTTATTATTATTGGTTTTATCGTGTCTAGTTATGATTCCCTTCTTTCCTTTTGCTATTTGTGCCTCCGTAAAAG
TGGTTCAGGAATATGAACGAGCGGTGATATTTCGGCTTGGCCGTTTGGTCTCTGGAGGGGCTAAAGGTCCAGGTATTTTC
TTTGTGATACCGTGCACTGATGAATACCGCAAAATTGATATACGCACAAAGTCTTTCGACGTTCCTCCTCAAGAAATTCT
AACAAGAGACAGCGTAACCGTAGCAATGGACGCCGTGGTTTACTACAGAATATTTGATGCTACGATGGCAGTTGCTAACG
TCGAAAATGCCGATGGAGCGACTCGTCTTTTGGCACAAACAACGTTAAGAAACATGCTTGGTACCCGAAGCCTGTCAGAG
ATCTTAACAGGCCGTGATCACATTACCCACGAAATGATGGAACACTTGGATAACGCAACGGATGCCTGGGGAATCAAAGT
GGAACGCATTGAAATTAAGGATGTTCGTCTTCCAATACAGCTACAAAGGGCAATGGCCGCGGAAGCCGAAGCGTCAAGAG
AAGCCAAAGCAAAAGTGATAGCAGCTGAAGGAGAAATGAATGCATCGATAAAGCTTAAGGAGGCAGCAGATGTTATGTCA
GGTTCACCTAATGCAATGCAATTACGATACTTGCAAACCCTGACTACCATAAGTGCGGAAAAAAATTCAACCATAGTTTT
CCCGCTTCCAATTGATATGCTCAGTACCGCGTTCAAGAAGTAA

Alignment

ORF - retro_cint_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.67 %
• Parental protein coverage: 93.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AERKAKFSGEDTE-YGCCGYALMGISVFIMILIFPLALCAGIKVVQEYERAVIFRLGRLVKGGAKGPGIF
          AE..A.F........G.CG..L...S...MI..FP.A.CA..KVVQEYERAVIFRLGRLV.GGAKGPGIF
Retrocopy AEQNARFDQNKAGGAGICGLLLLVLSCLVMIPFFPFAICASVKVVQEYERAVIFRLGRLVSGGAKGPGIF

Parental  FIIPCTDEYRKVDLRTVSFDVPPQEILTKDSVTISVDAVVYYRVQDATMSIANVENADGATRLLAQTTLR
          F.IPCTDEYRK.D.RT.SFDVPPQEILT.DSVT...DAVVYYR..DATM..ANVENADGATRLLAQTTLR
Retrocopy FVIPCTDEYRKIDIRTKSFDVPPQEILTRDSVTVAMDAVVYYRIFDATMAVANVENADGATRLLAQTTLR

Parental  NMLGTKSLSEVLTDREYISAGMQSTLDEATDPWGIKVERVEIKDVRLPVQLQRAMAAEAEAAREARAKVI
          NMLGT.SLSE.LT.R..I...M...LD.ATD.WGIKVER.EIKDVRLP.QLQRAMAAEAEA.REA.AKVI
Retrocopy NMLGTRSLSEILTGRDHITHEMMEHLDNATDAWGIKVERIEIKDVRLPIQLQRAMAAEAEASREAKAKVI

Parental  AAEGEMNASRKLKEAADVMSESPNSMQLRYLQTLTSISAEKNSTIIFPLPIDMLSTMMKK
          AAEGEMNAS.KLKEAADVMS.SPN.MQLRYLQTLT.ISAEKNSTI.FPLPIDMLST..KK
Retrocopy AAEGEMNASIKLKEAADVMSGSPNAMQLRYLQTLTTISAEKNSTIVFPLPIDMLSTAFKK

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_6 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_6 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	ENSCING00000000485	1 retrocopy	retro_cint_6 ,
Callithrix jacchus	ENSCJAG00000009137	1 retrocopy	retro_cjac_440,
Microcebus murinus	ENSMICG00000005517	1 retrocopy	retro_mmur_571,
Mus musculus	ENSMUSG00000028455	1 retrocopy	retro_mmus_1034,
Oryctolagus cuniculus	ENSOCUG00000006451	1 retrocopy	retro_ocun_695,