RetrogeneDB ID: retro_cint_25

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 2:2847323..2847674(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCING00000012473
• Aliases: None
• Description: None

Sequence

>retro_cint_25
ATGAAGTGGCAATTCAAGGTGGATCACACATACGAGCATCGTTGCAACGAGTCTTCTAAAATCATCACGAAGTATCCAAG
CCGTATCCCTGTGATTGTGGAAAAAGCGGAAGGTTCCACCATCCAGGACATTGATAAGAGAAAGTATCTTGTCCCAGCTG
ATATCTCGGTTGCTCAATTCATGTGGATCATCAGGAAACGTATTGACCTTTCTCCTGAGAAAGCAATCTTTCTCTTTGTT
GATAAAGTTGTCCCAAACTCATGCTCCACCATGGGAGCAATCTACGCAGAACACAAAGATGAAGATGGTTTCCTTTACAT
CGCTTACAGCGGTGAAAACACGTTCGGTTCA

Alignment

ORF - retro_cint_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKWQYKEEHTFDKRRTEGEKIRKKYPDRVPVIVEKAMKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL
          MKWQ.K..HT...R..E..KI..KYP.R.PVIVEKA....I.D.DK.KYLVP.D..V.QF...IRKRI.L
Retrocopy MKWQFKVDHTYEHRCNESSKIITKYPSRIPVIVEKAEGSTIQDIDKRKYLVPADISVAQFMWIIRKRIDL

Parental  RPEEALFFFVNNVIPPTSTTMGQLYQEHHEEDFFLYIAYSDESVYGA
          .PE.A.F.FV..V.P....TMG..Y.EH..ED.FLYIAYS.E...G.
Retrocopy SPEKAIFLFVDKVVPNSCSTMGAIYAEHKDEDGFLYIAYSGENTFGS

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

1 EST(s) were mapped to retro_cint_25 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV980484	2847320	2847440	97.5	113	3	110

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_25 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 18 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014883	1 retrocopy	retro_btau_905,
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25 ,
Callithrix jacchus	ENSCJAG00000016655	2 retrocopies	retro_cjac_2851, retro_cjac_3820,
Dipodomys ordii	ENSDORG00000005229	1 retrocopy	retro_dord_308,
Echinops telfairi	ENSETEG00000004652	7 retrocopies	retro_etel_1020, retro_etel_1078, retro_etel_1562, retro_etel_2068, retro_etel_493, retro_etel_666, retro_etel_976,
Gorilla gorilla	ENSGGOG00000013770	1 retrocopy	retro_ggor_821,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Mustela putorius furo	ENSMPUG00000010473	2 retrocopies	retro_mputfur_1290, retro_mputfur_258,
Mus musculus	ENSMUSG00000018567	1 retrocopy	retro_mmus_3107,
Nomascus leucogenys	ENSNLEG00000008049	2 retrocopies	retro_nleu_1670, retro_nleu_4,
Oryctolagus cuniculus	ENSOCUG00000006997	1 retrocopy	retro_ocun_311,
Otolemur garnettii	ENSOGAG00000004388	2 retrocopies	retro_ogar_1212, retro_ogar_1224,
Pongo abelii	ENSPPYG00000007901	1 retrocopy	retro_pabe_122,
Pan troglodytes	ENSPTRG00000034115	1 retrocopy	retro_ptro_60,
Rattus norvegicus	ENSRNOG00000017417	2 retrocopies	retro_rnor_1818, retro_rnor_2093,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,