RetrogeneDB ID: retro_csav_5

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_55:512568..513441(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000000691
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000000950
• Aliases: None
• Description: None

Sequence

>retro_csav_5
CTAATAAACCAAGTTATGCAAGAGGCCCAACCGAATTACGAAGCAAAACCGATGAATAACCAAACGGCAAATGTTAGATT
TGATCAGAAGGATTCTGGTGGTGTGAATTTGTGTGGTGGGATATTGATGTTTTTTGCCTGTATTTTGATTCTTGCTACAT
TACCATTAAGCATTTGGAACTGCATCAAAATGGTTCAAGAGTATGAACGGGCAGTAATATTTCGACTTGGACGCTTGGTA
TCCGGTGGTGCCAAAGGTCCCGGAATTTTCTTCATAATTCCTTGCACCGATGAATACCGCAAAGTCGACATGCGAACAAA
ATCGTTCGACGTCCCACCGCAAGAAATTCTAACGAAAGATAGTGTTACAGTCGCAATGGACGCAGTGGTATACTACAGGG
TCTTTGATGCGACCATGGCAGTTGCAAATGTCGAAAATGTGGACGGTGCAACCCGTCTACTGGCGCAAACAACGTTGCGT
AATATGCTTGGAACGCGAAGCCTAACAGAAATCCTTACTGGGCGCGACCACATCACCCATGAAATGATGAGCAGCCTCGA
CCAAGCAACTGACGTGTGGGGTATCAAAGTGGAGAGGATTGAAATCAAGGATGTTCGTCTTCCGGTGCAACTTCAACGAG
CAATGGCTGCCGAGGCTGAGGCTTCGAGAGAAGCTCGGGCAAAGGTAATTGCAGCCGAAGGAGAAATGAACGCATCTAAG
AAACTAAAAGAAGCTGCGGATATAATGGCTGGCGCACCGAACGCAATGCAATTGAGGTATCTTCAAACCCTCACCGCCAT
AAGTGCCGAGAAAAATTCGACCATCGTGTTTCCCCTTCCTATTGACATGATTGCATCCGCTCTAAAGAAGTAA

Alignment

ORF - retro_csav_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.82 %
• Parental protein coverage: 95.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QPYNNQI-NTSGDDADYG---CCGICLLILSGFIILLTFPVAICMCVKVVQEYERAVIFRLGRLSKGGAK
          .P.NNQ..N...D..D.G....CG..L.......IL.T.P..I..C.K.VQEYERAVIFRLGRL..GGAK
Retrocopy KPMNNQTANVRFDQKDSGGVNLCGGILMFFACILILATLPLSIWNCIKMVQEYERAVIFRLGRLVSGGAK

Parental  GPGIFFVIPCTDEYRKVDLRTVSFDVPPQEILTKDSVTISVDAVVYYRVQDATMSIANVENADGATRLLA
          GPGIFF.IPCTDEYRKVD.RT.SFDVPPQEILTKDSVT...DAVVYYRV.DATM..ANVEN.DGATRLLA
Retrocopy GPGIFFIIPCTDEYRKVDMRTKSFDVPPQEILTKDSVTVAMDAVVYYRVFDATMAVANVENVDGATRLLA

Parental  QTTLRNMLGTKSLSEVLTDREEISAGMQATLDIATDPWGIKVERVEIKDVRLPVQLQRAMAAEAEAARDA
          QTTLRNMLGT.SL.E.LT.R..I...M...LD.ATD.WGIKVER.EIKDVRLPVQLQRAMAAEAEA.R.A
Retrocopy QTTLRNMLGTRSLTEILTGRDHITHEMMSSLDQATDVWGIKVERIEIKDVRLPVQLQRAMAAEAEASREA

Parental  RAKVIAAEGEMNASRKLKEAADVMSESPNSMQLRYLQTLTAISAEKNSTIIFPLPIDMVTSLMTK
          RAKVIAAEGEMNAS.KLKEAAD.M...PN.MQLRYLQTLTAISAEKNSTI.FPLPIDM..S...K
Retrocopy RAKVIAAEGEMNASKKLKEAADIMAGAPNAMQLRYLQTLTAISAEKNSTIVFPLPIDMIASALKK

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_5 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_5 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009137	1 retrocopy	retro_cjac_440,
Ciona savignyi	ENSCSAVG00000000950	1 retrocopy	retro_csav_5 ,
Microcebus murinus	ENSMICG00000005517	1 retrocopy	retro_mmur_571,
Mus musculus	ENSMUSG00000028455	1 retrocopy	retro_mmus_1034,
Oryctolagus cuniculus	ENSOCUG00000006451	1 retrocopy	retro_ocun_695,