RetrogeneDB ID: retro_cint_1

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 12:4431723..4432818(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCING00000002406
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000003305
• Aliases: None
• Description: None

Sequence

>retro_cint_1
ATGGGGATATTGGAAAAGATTTCTGAGATTGAAAAAGAAATTCAGAGAACTCAAAAAAATAAAGCAACTGAATACCATCT
GGGATTGTTGAAAGCAAAACTCGCAAGATATCGAGCACAGCTATTAGAAGGGTCCAAGACATCAGGTCCTAAAGGAGAGG
GCTTCGATGTTATGAAATCAGGGGATGCAAGAGTAGCATTGGTCGGATTTCCTTCAGTTGGTAAATCTACTTTGCTATCA
ACATTAACCTCTACTACCAGCGAGTGTGCTTCGTACGAGTTCACAACTTTAACCTGCATCCCTGGTGTGATAGAGCATAA
CGGGGCAAGCATCCAACTTCTGGATCTTCCAGGGATTATAGAAGGAGCTGCTGCTGGTAAAGGAAGAGGAAGACAGGTCA
TCTCGGTTGCTCGGACTGCCGACATTGTTGTGATGATGTTGGATGCTTTGAAAGGTGACATCCAAAAGGAGCTGCTTACA
AAAGAACTGGAAGCTGTCGGAATAAGGCTGAATAAGAAGCGGCCGAATATTTATTTCAAGGAGAAAAAAGGTGGAGGGAT
TTCTATAACTGCTACTTGCATTCTGACCAAAATATCAGAAAGGATGATCAATCTTATACTTCATGAGTACAAGATATTCA
ATGCAGATGTGGTGTTTAGGGATGACTGCGGCACGGAAGAGTTTATTGATGTTGTGGTGGGAAAGCGAAAATACATGCCA
TGTTTATATGTCTACAACAAGATCGATCAAATCTCCATTGAAGAAGTTGATCGTATTGCATGGCAACCTCACTGTGTTGT
CATTAGTTGCAATATGTTGCTAAACCTGGAGCATTTAAAAGAAATGATCTGGAGATATCTGCATTTGATTACTGTTTACA
CCAAGAAACCCGGGAAGAAACCAGACTTTAATGATGGTCTCATCTTGCGTTCGAATTGCACCGTAGAACATGCATGCCAT
GCCATTCATAGGACTCTGGTTCAGAATTTTAAATACGCTCAGGTTTGGGGCCACAGCGCTAAGTATAATGGACAGCACGT
GGGGTTATCGCATAAATTGTCTCATGAGGATGTTTTGCTTGTTACGAAAAAGTAA

Alignment

ORF - retro_cint_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.46 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSILTKISEIEAEMARTQKNKATAGHLGMLKARLAKLKRELITPKGGAGGGTGEGFDVAKTGDARIGFVG
          M.IL.KISEIE.E..RTQKNKAT..HLG.LKA.LA.....L........G..GEGFDV.K.GDAR...VG
Retrocopy MGILEKISEIEKEIQRTQKNKATEYHLGLLKAKLARYRAQLLEGSK-TSGPKGEGFDVMKSGDARVALVG

Parental  FPSVGKSTLLSNIAGVYSEVASYEFTTLTTVPGVIKYKGAKIQLLDLPGIIEGAKDGKGRGKQVIAVART
          FPSVGKSTLLS......SE.ASYEFTTLT..PGVI...GA.IQLLDLPGIIEGA..GKGRG.QVI.VART
Retrocopy FPSVGKSTLLSTLTSTTSECASYEFTTLTCIPGVIEHNGASIQLLDLPGIIEGAAAGKGRGRQVISVART

Parental  CSLIFIVLDVLKPLGDKRLIEKELEGFGIRLNKKPPNIHYKMKEKGGINFQAMVPQSELDAELAKKILSE
          .......LD.LK....K.L..KELE..GIRLNKK.PNI..K.K..GGI...A..............IL.E
Retrocopy ADIVVMMLDALKGDIQKELLTKELEAVGIRLNKKRPNIYFKEKKGGGISITATCILTKISERMINLILHE

Parental  YRIHNADIILKEDCVTDDLIDVVEGNRVYIPCLYLLNKIDQISIEELDIIYKVPHCVPISAHHKWNFDDL
          Y.I.NAD.....DC.T...IDVV.G.R.Y.PCLY..NKIDQISIEE.D.I...PHCV.IS.....N...L
Retrocopy YKIFNADVVFRDDCGTEEFIDVVVGKRKYMPCLYVYNKIDQISIEEVDRIAWQPHCVVISCNMLLNLEHL

Parental  LERMWEYLRLVRIYTKPKGQLPDYEAPVVLNSDKCSVEDFCNKIHRTLLKQFKHALVWGSSVKYNPQSVG
          .E..W.YL.L...YTK..G..PD......L.S..C.VE..C..IHRTL...FK.A.VWG.S.KYN.Q.VG
Retrocopy KEMIWRYLHLITVYTKKPGKKPDFNDGLILRSN-CTVEHACHAIHRTLVQNFKYAQVWGHSAKYNGQHVG

Parental  KEHVLMDEDVVQIVKR
          ..H.L..EDV....K.
Retrocopy LSHKLSHEDVLLVTKK

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

19 EST(s) were mapped to retro_cint_1 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AJ493863	4431839	4432052	97.7	208	5	203
AV975348	4431667	4432261	99.9	593	1	592
BP013756	4431756	4432114	98.1	354	4	349
BW197810	4431920	4432264	98.9	338	4	334
BW201532	4431728	4432258	99.3	524	4	520
BW210348	4431731	4432225	99.2	490	4	486
BW220348	4431731	4432235	99.9	503	1	502
BW281356	4431691	4432107	99.8	410	1	409
BW290164	4431678	4432266	99.7	586	2	584
BW293915	4431706	4432313	98.2	595	11	584
BW305519	4431731	4432265	100	534	0	534
BW327671	4431674	4432281	99.7	594	2	591
BW331761	4431671	4432264	98.2	578	10	566
BW336927	4431665	4432272	99.9	605	1	604
BW342645	4431673	4432266	99.9	592	1	591
BW360183	4431674	4432268	99.7	592	2	590
BW364996	4431671	4432258	98.2	576	11	565
FF868937	4432125	4432403	99.7	277	1	276
FG000050	4431871	4432377	97.7	501	0	493

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_1 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007040	1 retrocopy	retro_amel_1448,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1 ,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,