RetrogeneDB ID: retro_csav_28

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_51:1083566..1084191(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000003638
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000000194
• Aliases: None
• Description: None

Sequence

>retro_csav_28
TTAACCAGGATGGAAATCACCAGCAACAGTGTTCTCATGGTTTTAGCTGGTTATGAGACTTCTGCAAACTTAATGTGCTT
TCTAGCTTATAACCTTGCTGTCTATAAAGAAGCCCAGAGAATGGTACAAGAGGAAATTTCCCACACTCTAGAGGAGTATG
GATCATTTACATACGAAGCATTAAACAGCATGAAGTATTTGACTTCGTGTATACAAGAAACCTTGAGGCTGTACCCACCA
ATAGCTATTAATTCTCGCTTTCCCATAAAAGACATAACCATCAACGGCATATTCTTTCAAAAGGGAATACAAGTCAACAT
ACCTGTCTATGGACTAAGCCGAGATGATGAAATATGGGATGAACCATTGAATTTCAAACCGGAACGGATGTCAGATATGT
CCAAGATCAACTCCATGGTATTTCAGCCCTTTGGTGGTGGGCCTCGGTGGTTGTATCGGCATGCGATTCGCGCTTCTGGA
AATTAAGCTCGTCTTCTGCAAATTTCTACAGCAGTTTAACATTGATGTGTGTGAGGATACTCCAGAGCCGCCCTTAGCTA
TGTTGTTTAGATCTACAACACTTAAGCCAAAGGAGAATATTTTTTTGAAATTATCGAGGAGGGAA

Alignment

ORF - retro_csav_28 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.5 %
• Parental protein coverage: 95.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTRVEIKGNSLIFIFGGYETTSNAMLFLAYNLALHKDAQHHVREEVQAALHKHGGLTYEAIQDLKYMTQC
          .TR.EI..NS......GYET..N.M.FLAYNLA..K.AQ..V.EE....L...G..TYEA....KY.T.C
Retrocopy LTRMEITSNSVLMVLAGYETSANLMCFLAYNLAVYKEAQRMVQEEISHTLEEYGSFTYEALNSMKYLTSC

Parental  LNESLRLYPLTPMNSRYCEQDITINGITIPRGATVGIPMFGMMRDEDIWEDPLIFNPDRMEDMSKIDPMI
          ..E.LRLYP....NSR....DITINGI....G..V.IP..G..RD..IW..PL.F.P.RM.DMSKI..M.
Retrocopy IQETLRLYPPIAINSRFPIKDITINGIFFQKGIQVNIPVYGLSRDDEIWDEPLNFKPERMSDMSKINSMV

Parental  YQPFGAGPR-NCIGMRFALLEIKITFAKLLLKFDLDVCEDTPEPPLAVTFK-TSMRPKETLYLKVVGRE
          .QPFG.GPR..CIGMRFALLEIK..F.K.L..F..DVCEDTPEPPLA..F..T...PKE...LK...RE
Retrocopy FQPFGGGPR>GCIGMRFALLEIKLVFCKFLQQFNIDVCEDTPEPPLAMLFRSTTLKPKENIFLKLSRRE

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_28 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_28 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	ENSCSAVG00000000194	1 retrocopy	retro_csav_28 ,