RetrogeneDB ID: retro_csav_15

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_1:3473725..3474556(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000010860
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000008837
• Aliases: None
• Description: None

Sequence

>retro_csav_15
GTACATATAAATGCTCGCTCTGTCCTGTACCCTCAATCCAGCTGTAAAAGATTTCCTGTTCCTGATGGTAAAGTTAGTTG
GAAAGTTGGTTTTAAAGAATACACTCCTGTCAACCACACAGCGCCAATCGTAGCATCCAACCCCCCATGGGCCGATGTTG
ATGTCACCAAGAGTCCACTGAACATCTTAAAGTACAATGCCATTGACGGAAAAACAAATCGTAAAAGTTTCACAGGGGTC
TATGATGTAATAAACAATGTTCCGATTAACCCAGCAGGGAGAACAGGGGTTACCGGACGTGGGTTGCTTGGAAAATGGGG
ACCGAACCATGCAGCTGATCCCATTGTGACACGCTGGAAATGCAATGAAGGGGTTATCGTGAAACATGTAAAAACAAAGC
TACCTGTCCTCCAATTTGTTGCTATTCAGAGGAAGGACAATGGTGAATGGGCGATACCAGGTGGAATGGTGGATGCTGGT
GAGAGAGTTTCGGTTACGTTAAAGCGTGAATTCGGAGAGGAAGCATTAAATGCATTGGATAACAAAGCTGACAACGCAAA
AATCAACAAACTAATCAAAGAGCTTTTTAAATCAGGAAAAACAGTCTTTGAGGGGTATGTGGATGACCCAAGGAACACTG
ACAATGCGTGGATGGAGACTGTGGCCGTTAATTTCCACGACGATAATGGGAACAGTGTTGCCAAATTACCGCTAAGCGCC
GGTGACGATGCAGGTGCGGTTCGTTGGATGGATGTGGGGAGGGAACTAATGCTCTATGCTTCGCATAAACAGTTTTTGAA
GCAAACAGCTAAAAATTTAGCTGCCCATTGG

Alignment

ORF - retro_csav_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.42 %
• Parental protein coverage: 97.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHINSRSPEYPGSKIKRFVVPDKSVSWSVPLPGYNPPQYTSPAVKSQPIWADPPLEPQPTGSTVSLPFNA
          VHIN.RS..YP.S..KRF.VPD..VSW.V....Y.P...T.P.V.S.P.WAD......P......L..NA
Retrocopy VHINARSVLYPQSSCKRFPVPDGKVSWKVGFKEYTPVNHTAPIVASNPPWADVDVTKSPLNI---LKYNA

Parental  DDKERNVSRKSFTGKYKVVGGLPRNPSGRTGLTGRGLLGRYGPNHAADPVVTRWERDETGTVIKIHGK-P
          .D...N..RKSFTG.Y.V....P.NP.GRTG.TGRGLLG..GPNHAADP.VTRW...E...V.....K.P
Retrocopy IDGKTN--RKSFTGVYDVINNVPINPAGRTGVTGRGLLGKWGPNHAADPIVTRWKCNEGVIVKHVKTKLP

Parental  VLQFVAICRNDTGEWAIPGGMVDAEENITQTLKREFSEEVLLDVDDQKPGTEIQTQLNKLFNSGVKVYEG
          VLQFVAI.R.D.GEWAIPGGMVDA.E....TLKREF.EE.L...D.......I......LF.SG..V.EG
Retrocopy VLQFVAIQRKDNGEWAIPGGMVDAGERVSVTLKREFGEEALNALDNKADNAKINKLIKELFKSGKTVFEG

Parental  YSDDHRNTDISWIETSVFNFHDDNGSTFDRIKLHPGEETSGVQWKRIDQSINLFASHFQFLEKVAKMHNA
          Y.DD.RNTD..W.ET...NFHDDNG.......L..G.....V.W........L.ASH.QFL...AK...A
Retrocopy YVDDPRNTDNAWMETVAVNFHDDNGNSVAKLPLSAGDDAGAVRWMDVGRELMLYASHKQFLKQTAKNLAA

Parental  HF
          H.
Retrocopy HW

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_15 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_15 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000008837	1 retrocopy	retro_csav_15 ,
Echinops telfairi	ENSETEG00000019164	1 retrocopy	retro_etel_348,
Monodelphis domestica	ENSMODG00000020738	2 retrocopies	retro_mdom_157, retro_mdom_706,
Oryctolagus cuniculus	ENSOCUG00000002670	2 retrocopies	retro_ocun_1045, retro_ocun_990,