RetrogeneDB ID: retro_cint_30

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: HT000119.1:139016..140124(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000001594
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000007560
• Aliases: None
• Description: None

Sequence

>retro_cint_30
ACAAAGAAAAAACAGGGTGTTTTGGATCGGCTTAAACAAGGTCCCATAGTAGGCGATGGTAGCATGTGTATGACATTGGA
AAAAAGAGGTTACTGCAGGGCTGGACCGTGGACGCCCGAATCTGTTTTGATCTACCCCGACGCCGTGAAGCAACTGCTTC
GTGAATACGTTAGAGCTGGGGCTGATGTTATACAAACCCCGTGCTTTTATTGCTCCGATGGGATGATTAAAAGAGGAGCG
GGCGGGGAAGAAACCGTATCGTATACAACAGCGGCAATCAACGAGGCTGCTTGCAAACTTGCGCACGAAGTTGCGAGTGA
AGGAGAGGTTTTAGTTTGTGGCGGATTGTCCCCTGTATTTCTTTCTCAAAGAAAGAGATTTCGAAAAGACCAGATTGGAA
TTCAAGGCTCAACTTGATGTGTTTATTAAATACAAAGTTGATTTTGTGTTGGCTGAGTTCTTCAGATGCGTTGAAGAAAT
TGAGATATGTGTTGACGTAATGAAACGTGCGAACATACCTATTGCTTGTACAATGGCCCTTGGTCCACTAGGTGACCATA
ATGATGTTTCTGTGGAAGAATGTGCGATCAGGATGGCAAAATCTGGTGCTGATATCATTGGTATCAACTGCCTGTTTGAT
TTCGACACCTGCTTAAAAACTTTGAAGATAATGAAGGATGCTTTGGATGGTGAAGGCTTATCGACACCACTGATGTGCCA
ACCACTAGGTTGGAGGTGTCCGGAGGTTGAGAACACCAAGATGGGATATCTGGATCTTCCCGAAACCCCCCTAGCTTTAG
ACCCACGCACAGCAACAAGGTTTGAGGTCCACAAGTTTACTCGGGCAGCATACAATCTTGGGGTGCGTTATATAGGTGGT
TGTTGTGGTATGGAACCTCACCATATTAGGGCAATCGCTCACGAGCTTGCACCAGAAAGGAAGAGGAATCCACCCGCACA
AGACATGTGCCCACCCCTCGGCTACCTTCAATACAGTGGGCTATCTAATATTAAAACCAAAACATGTCCCAAGTATTGGA
GTGACATGAAGCCTGGTAGTGGTCGGCCGTATAACCCAGCGTGCTCAATGGGTCAAGATGGACATTGG

Alignment

ORF - retro_cint_30 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.15 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TAQKKGLLERLKEGPVVGDGSMCMTLEKRGYCRAGPWTPEAVIAYPDAVKQLLREYLRAGADVLQTPCFY
          T..K.G.L.RLK.GP.VGDGSMCMTLEKRGYCRAGPWTPE.V..YPDAVKQLLREY.RAGADV.QTPCFY
Retrocopy TKKKQGVLDRLKQGPIVGDGSMCMTLEKRGYCRAGPWTPESVLIYPDAVKQLLREYVRAGADVIQTPCFY

Parental  CSDGMLKKGTASGETVAYTTDAINEAACKIAHEVAAEGNALVCGGLS-PVLSY-LRERDSAKTRAEFDAQ
          CSDGM.K.G....ETV.YTT.AINEAACK.AHEVA.EG..LVCGGLS.P..S..L.ERD..KTR.EF.AQ
Retrocopy CSDGMIKRGAGGEETVSYTTAAINEAACKLAHEVASEGEVLVCGGLS<PCISF<LKERDFEKTRLEFKAQ

Parental  LDVFIKYKVDFVLAEFFAHVEELEICVDVMKKAKMPIACSMRIGPMGDSNGVSVEECAVRMAKTGADLIG
          LDVFIKYKVDFVLAEFF..VEE.EICVDVMK.A..PIAC.M..GP.GD.N.VSVEECA.RMAK.GAD.IG
Retrocopy LDVFIKYKVDFVLAEFFRCVEEIEICVDVMKRANIPIACTMALGPLGDHNDVSVEECAIRMAKSGADIIG

Parental  INCLYDFDTCLKTLKRMRDALDKEGLKTPLMCQPLGWRCPEVEDKLIGYLDLPETPLALDPRTATRFEVH
          INCL.DFDTCLKTLK.M.DALD.EGL.TPLMCQPLGWRCPEVE....GYLDLPETPLALDPRTATRFEVH
Retrocopy INCLFDFDTCLKTLKIMKDALDGEGLSTPLMCQPLGWRCPEVENTKMGYLDLPETPLALDPRTATRFEVH

Parental  EFTRAAYNLGTRYIGGCCGMEPHHIRAIAQELAPERKRDPPVQDMCPPTGFMQFSGLSNIKEKASMDFWT
          .FTRAAYNLG.RYIGGCCGMEPHHIRAIA.ELAPERKR.PP.QDMCPP.G..Q.SGLSNIK.K.....W.
Retrocopy KFTRAAYNLGVRYIGGCCGMEPHHIRAIAHELAPERKRNPPAQDMCPPLGYLQYSGLSNIKTKTCPKYWS

Parental  NTKPGSGRPFNPASTQTEGGRF
          ..KPGSGRP.NPA......G..
Retrocopy DMKPGSGRPYNPACSMGQDGHW

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

4 EST(s) were mapped to retro_cint_30 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM960887	138996	139506	97.1	497	10	485
BW199450	138954	139547	97.6	561	10	548
BW209765	138966	139562	97.3	576	11	561
FK226737	139035	139565	97	519	10	505

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_30 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	ENSCING00000007560	1 retrocopy	retro_cint_30 ,
Monodelphis domestica	ENSMODG00000019726	1 retrocopy	retro_mdom_1533,
Mus musculus	ENSMUSG00000074768	1 retrocopy	retro_mmus_192,
Rattus norvegicus	ENSRNOG00000011200	1 retrocopy	retro_rnor_2137,
Tursiops truncatus	ENSTTRG00000012963	1 retrocopy	retro_ttru_489,