RetrogeneDB ID: retro_ttru_1491

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_114643:119564..120710(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKAP2
• Ensembl ID: ENSTTRG00000009624
• Aliases: None
• Description: cytoskeleton associated protein 2 [Source:HGNC Symbol;Acc:1990]

Sequence

>retro_ttru_1491
AGCTCTGCAACAATGAAGAGACTTTCAGCTACTGTCTCTAAAGCCACAAAGTCTCAGCCTGTAGACACCAGCAGCGTAAC
AGTGAAAAGTGATAGAGCCTCACATACGACGACTGCCGCTAAATTTGTGAGCACTACATCTCAGAGCAGTCAACTTGTGC
GACCTTCTATTAGAAGTCACCACAGTAATAACCAGGACACCATGAAACAAGGCATCAGTAGGATGTCTGCCAGTGTTACA
GTTTGGAAAGGACCTCGAGAGAAAGAATTATTACAGTTAAACACAGCTTCGTCTATTATCAAAACCAGTTCTTCTCAGGA
CATAGAAAGAAATAAGACACTATCAAGAAGCATGACATCTGAAATGGTAGCCAGGCCTGCTTCGTCTTCTAATACTTAAC
TGAGAGAAAAGTCAAAAAGCATTGACCAGTGCAGATATACCACGGTGAAAGCAGCTATTGACAGTAGATGGACTCAGCGC
AGAGAAACTGCGGAGGAGAGAAAGGCTCGTCTGAGTGAGTGGAAAGCTAGCAAAGGAAGAGTGATGAAAAGGCCTCCCAG
CTCAGTGGTTACCCAGCCTGTGCCCGAAGCACGAAATGAAAAACCAGTTGGGTCCTTCTGGACTGCCACGGCTGAAGAAG
ACGAACAACGATTGTTGACTGAAAAAGTAAACAAGACATTTTCTGAATGCCTAAACCTGATTAATGAGGGATATCCAAAA
GAAGAAGTATTGGTTACACTGAATGACCTGATTAAAAATATTCCAGATGCCAAAAATCTTGTTAAACATTGGATATGCCT
GCTTGTACTGAACCACTTATGAGTCCTATTGAAAATATTACTGCAATCTATGAGAAGGCCATCCTGGCAGGAGCTCAGCC
TATTGAAGAGATGCGACAGGCAACTGTTGACATTCTGACAATGAAGAGTCAAGAAAAAGTTAAATTTGGAGAAAATATTG
GGGAGTCTTGTGCAACCAAGGAACAAATCCAAGAAGCCACCATTGATGATATAAGTGTTAATCTGGGGTCAGAAAAACCG
GAAAGAGAAAATAAGCATCTTACGAATGTAGTATTTCAAAGTTGTGAAAAAAGAGCAAGATAGCAAAACAAAAGGTCCAA
CCAGTGATGTTAAAACCCGCAATACA

Alignment

ORF - retro_ttru_1491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.24 %
• Parental protein coverage: 55.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSAATKKLSATVSKATKSQPVHASSVTVKSDRASHMTTATKFVSTTSQSSQLVRPSIRSHHSNNQNTMKQ
          SSA..K.LSATVSKATKSQPV..SSVTVKSDRASH.TTA.KFVSTTSQSSQLVRPSIRSHHSNNQ.TMKQ
Retrocopy SSATMKRLSATVSKATKSQPVDTSSVTVKSDRASHTTTAAKFVSTTSQSSQLVRPSIRSHHSNNQDTMKQ

Parental  DISRTSASVTVRKGPREKELLQLNTVSSIIKTSSSQDIKRNKTLSRSMTSEMVARPASSSNTKLIEKSKS
          .ISR.SASVTV.KGPREKELLQLNT.SSIIKTSSSQDI.RNKTLSRSMTSEMVARPASSSNT.L.EKSKS
Retrocopy GISRMSASVTVWKGPREKELLQLNTASSIIKTSSSQDIERNKTLSRSMTSEMVARPASSSNT*LREKSKS

Parental  IDQRRHTMVKAAIDSRWTQPRETAEERKARLSEWKAGKGRVMKRPPSSVVTQPEPEAQNEKPVGSFWTTM
          IDQ.R.T.VKAAIDSRWTQ.RETAEERKARLSEWKA.KGRVMKRPPSSVVTQP.PEA.NEKPVGSFWT..
Retrocopy IDQCRYTTVKAAIDSRWTQRRETAEERKARLSEWKASKGRVMKRPPSSVVTQPVPEARNEKPVGSFWTAT

Parental  AEEDEQRVFTEKVNKTFSECLNLINEGCPKEEVLVTLNDLIKNIPDAKKLVKYWICL-ARVEPLTSPIEN
          AEEDEQR..TEKVNKTFSECLNLINEG.PKEEVLVTLNDLIKNIPDAK.LVK.WICL.A..EPL.SPIEN
Retrocopy AEEDEQRLLTEKVNKTFSECLNLINEGYPKEEVLVTLNDLIKNIPDAKNLVKHWICL<ACTEPLMSPIEN

Parental  VIAIYEKAILAGAQPIEEMRHAIVDILTMKSQEKVKFGENIEEACATKEQIQEATTDDTSVNLGSEKPEI
          ..AIYEKAILAGAQPIEEMR.A.VDILTMKSQEKVKFGENI.E.CATKEQIQEAT.DD.SVNLGSEKPE.
Retrocopy ITAIYEKAILAGAQPIEEMRQATVDILTMKSQEKVKFGENIGESCATKEQIQEATIDDISVNLGSEKPER

Parental  ENKHPRNVVFQGCE-KEQDDKTKDPTSDVKTPNT
          ENKH..NVVFQ.CE.KEQD.KTK.PTSDVKT.NT
Retrocopy ENKHLTNVVFQSCE>KEQDSKTKGPTSDVKTRNT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1491 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1491 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005898	1 retrocopy	retro_cfam_968,
Choloepus hoffmanni	ENSCHOG00000009905	2 retrocopies	retro_chof_1493, retro_chof_973,
Cavia porcellus	ENSCPOG00000012382	1 retrocopy	retro_cpor_171,
Felis catus	ENSFCAG00000010021	1 retrocopy	retro_fcat_1770,
Myotis lucifugus	ENSMLUG00000000132	1 retrocopy	retro_mluc_1515,
Monodelphis domestica	ENSMODG00000010436	1 retrocopy	retro_mdom_1364,
Mustela putorius furo	ENSMPUG00000017996	1 retrocopy	retro_mputfur_1270,
Mus musculus	ENSMUSG00000037725	1 retrocopy	retro_mmus_2651,
Otolemur garnettii	ENSOGAG00000008428	1 retrocopy	retro_ogar_1743,
Tupaia belangeri	ENSTBEG00000005807	1 retrocopy	retro_tbel_176,
Tursiops truncatus	ENSTTRG00000009624	2 retrocopies	retro_ttru_1491 , retro_ttru_1741,