RetrogeneDB ID: retro_cint_27

Retrocopy location

• Organism: Vase tunicate (Ciona intestinalis)
• Coordinates: 5:3924797..3925925(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKM
• Ensembl ID: ENSCING00000007141
• Aliases: None
• Description: creatine kinase [Source:RefSeq peptide;Acc:NP_001027661]

Sequence

>retro_cint_27
AACACCAACACTGCCCGCTACACCGCTAGTGAAGAATTCCCTGACCTATCCAAGCACAACAACCACATGTCTAGATGTCT
CACCGAAGAAATCTACAAGAAAATGCGAGCAGTCCAGACTCCCAATGGTTACACCATTGACTCTGCAATCCAAACTGGCG
TTGACAATCCAGGGCATCCTTTCATCATGACTGTTGGTTGCGTCGCCGGAGATGAAGAATCATACGAAGTCTTCGCCGAC
CTGTTTGACCCAGTTATCGAGGCTCGACACAACGGTTACAAGAAAACCGACATGCACAAGACCGACATCGATCCAACCCA
CTTGAAAGGAGGCACCAACATGGACCCAAAATACGTGCTTTCATCTCGAGTCCGCACTGGACGCAGCATCCGTGGCTTGT
GTCTTCCACCTCACTGCAGCCGTGCTGAGCGCCGCAAGGTCGAGCAGATTTCGTGCGAGGCCCTGGCTAAGTTGGATGGC
GACCTTAAAGGCAAGTATTACCCACTAAAGGGAATGAGTGAGGAACACCAGGATCAACTCATCAATGATCATTTCCTCTT
CGACAAGCCCGTCTCTCCTCTTCTGCTCGCATCCAACATGGCACGTGACTGGCCCGACGCACGGGGAATCTGGCACAATG
ACAAAAAGAACTTCTTGGTTTGGGTGAATGAAGAAGATCATCTTCGAGTCATCTCAATGGAAAAGGGTGGCAACATCAAC
GAAGTATTCAAGAGATGGTGCACCGGTCTTCAACTTGTTGAGAAGTACATGAAGGAGAGTGGTTACGAATACATGTGGAA
CTCACATCTTGGATACGTCCTTACTTGCCCAAGCAACCTCGGCACAGGTGTGCGAGCTGGTGTGCACTTGAAGATCCCAT
TGATGTCCAAGTGTCCGCAGTTTGACGAAGTGCTTGGTAAACTTCGCCTGCAAAAGCGTGGAACTGGTGGAGTAGACACT
GCTTCAGAGGGCGGTACATTTGACATCTCTAACGCTGATCGTATCGGTTTCTCCGAAGTTGAGCTTGTGCAGATGGTCAT
CGATGGTGTTGAGTTTCTCATCGAATGCGAGAAGAAACTTGAGAAGGGCGAGAGCCTCGAAAGCGACATTAAGGGCCTTA
AGCAAAAA

Alignment

ORF - retro_cint_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.82 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKNCANFKDDEEYPDLSTHNNHMAHALTLPVFAKLRSKVTPSGFTLDQAIQTGVDNPGHPFIMTVGCVAG
          N.N.A.....EE.PDLS.HNNHM...LT.....K.R...TP.G.T.D.AIQTGVDNPGHPFIMTVGCVAG
Retrocopy NTNTARYTASEEFPDLSKHNNHMSRCLTEEIYKKMRAVQTPNGYTIDSAIQTGVDNPGHPFIMTVGCVAG

Parental  DEESYEVFADLFDPVIEARHNGYKKTDMHKTDIDPTHLKGGTNMDPKYVLSSRVRTGRSIRGLCLPPHCS
          DEESYEVFADLFDPVIEARHNGYKKTDMHKTDIDPTHLKGGTNMDPKYVLSSRVRTGRSIRGLCLPPHCS
Retrocopy DEESYEVFADLFDPVIEARHNGYKKTDMHKTDIDPTHLKGGTNMDPKYVLSSRVRTGRSIRGLCLPPHCS

Parental  RAERRKVEQISCEALAKLDGDLKGKYYPLKGMSEEHQDQLINDHFLFDKPVSPLLLASNMARDWPDARGI
          RAERRKVEQISCEALAKLDGDLKGKYYPLKGMSEEHQDQLINDHFLFDKPVSPLLLASNMARDWPDARGI
Retrocopy RAERRKVEQISCEALAKLDGDLKGKYYPLKGMSEEHQDQLINDHFLFDKPVSPLLLASNMARDWPDARGI

Parental  WHNDKKNFLVWVNEEDHLRVISMEKGGNINEVFKRWCTGLQLVEKYMKESGYEYMWNPHLGYVLTCPSNL
          WHNDKKNFLVWVNEEDHLRVISMEKGGNINEVFKRWCTGLQLVEKYMKESGYEYMWN.HLGYVLTCPSNL
Retrocopy WHNDKKNFLVWVNEEDHLRVISMEKGGNINEVFKRWCTGLQLVEKYMKESGYEYMWNSHLGYVLTCPSNL

Parental  GTGVRAGVHLKIPLMSKCPQFDEVLGKLRLQKRGTGGVDTASEGGTFDISNADRIGFSEVELVQMVIDGV
          GTGVRAGVHLKIPLMSKCPQFDEVLGKLRLQKRGTGGVDTASEGGTFDISNADRIGFSEVELVQMVIDGV
Retrocopy GTGVRAGVHLKIPLMSKCPQFDEVLGKLRLQKRGTGGVDTASEGGTFDISNADRIGFSEVELVQMVIDGV

Parental  EFLIECEKKLEKGESLESDIKALKQK
          EFLIECEKKLEKGESLESDIK.LKQK
Retrocopy EFLIECEKKLEKGESLESDIKGLKQK

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

No EST(s) were mapped for retro_cint_27 retrocopy.

TSS

Ciona intestinalis was not studied using FANTOM5 data.

Lab

retro_cint_27 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 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018277	5 retrocopies	retro_cfam_1828, retro_cfam_2061, retro_cfam_2159, retro_cfam_274, retro_cfam_664,
Ciona intestinalis	ENSCING00000007141	1 retrocopy	retro_cint_27 ,
Echinops telfairi	ENSETEG00000008667	1 retrocopy	retro_etel_1667,
Macropus eugenii	ENSMEUG00000002979	3 retrocopies	retro_meug_1069, retro_meug_1569, retro_meug_2156,
Mus musculus	ENSMUSG00000001270	4 retrocopies	retro_mmus_1460, retro_mmus_1578, retro_mmus_1647, retro_mmus_2390,
Oryctolagus cuniculus	ENSOCUG00000008818	1 retrocopy	retro_ocun_1562,
Sarcophilus harrisii	ENSSHAG00000016459	2 retrocopies	retro_shar_432, retro_shar_645,