RetrogeneDB ID: retro_ttru_1741

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_89462:1558..2735(-)
• 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_1741
TCTGCCAGTGTTACAGTTTGGAAAGGGCCTCGAGAGAAAGAATTATTACAGTTAAATACACTTTCGTCTATTATCAAAAC
CAGTTCTTCTCAGGACATAAAAAGAAATAAGACACTATCAAGAAGCATGACATCTGAAATGGTAGCCAGACCTGCTTTGT
CTTCTAATACTAAACTGACAGAAAAGTCAAAAAGCATTGACCACCACAGACATACCATGGTGAAAGCAGCTATTGATAGT
AGATGGACTCAGCCCAGAGAAACTGCAGAGGAGAGAAAGGCTCGTCTGAGTGAGTGGAAAGCTGGCAAAGGAAGAGTGAT
GAAAAGGCCTCCGAGCTCAGTGGTTACCCAGCCTGAGCCCGAAGCACACAATGAAAAACTAGTTGGGTCCTTCTGGACTA
CCATGGCAGAAGAAGATGAACAACGATTGTTTACTGGAAAAGTAAACAAGACATTTTCTGAATGCCTACACCTGATTAAT
GAGGGATGTCCAAAAGAAGAAGTATTGGTTACACTGAATGACCTGATTAAAAATATTCCAGATGCCAAAAAACATGTTAA
ATATTGGATATGCCTTGCGCATATTGAACCACTTACAAGTCTACTGAAAATATTTTTGCAATCTATGAGAAGGCCATTCT
GGCAGGAGCTCAGCCTACTGAAGATATGCGACATGCCATTGTTGACATTCTGACAATGAAGAGTCAAGAAAAAGTTAAAT
TTGGAGAAAATATTTAGGAGGCTTGTGCAACCAAGGAACAAATCCAAGAAAACACCATTGATGATATAAGTGTTAATCTG
GGGTCAGAAAAACCAGAAATAGAAAATAAGCATCTTAGGAATGTGGTATTTCAAGGTTGTGAAAAAGAGCAAGATGACAA
AACAAAAGATCCAACCAGTGATATTAAAACCCCCAATACAGAAACTAGGGCAGGTTGCTTAATTAAATATAATGTGTCTA
CTTCTCCATACTTGCAAAGTGTGAAAAAAAGATGCAGTTTAACAAAACCAATTCTGCATTTAAAGAGCTAAAGATTCTCA
CACCAGTTAGACATTCACAATGTCTTCAAGAGAAGACTTCTAAATTGCCAGATATGTTAAAAGACCATTATCCTTGTGTG
TCTTCACTGGAACAGTTAACAGAGTTGGGAAGTGAAACTGACGCTTTTGTGTGCCGC

Alignment

ORF - retro_ttru_1741 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.89 %
• Parental protein coverage: 57.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SASVTVRKGPREKELLQLNTVSSIIKTSSSQDIKRNKTLSRSMTSEMVARPASSSNTKLIEKSKSIDQRR
          SASVTV.KGPREKELLQLNT.SSIIKTSSSQDIKRNKTLSRSMTSEMVARPA.SSNTKL.EKSKSID..R
Retrocopy SASVTVWKGPREKELLQLNTLSSIIKTSSSQDIKRNKTLSRSMTSEMVARPALSSNTKLTEKSKSIDHHR

Parental  HTMVKAAIDSRWTQPRETAEERKARLSEWKAGKGRVMKRPPSSVVTQPEPEAQNEKPVGSFWTTMAEEDE
          HTMVKAAIDSRWTQPRETAEERKARLSEWKAGKGRVMKRPPSSVVTQPEPEA.NEK.VGSFWTTMAEEDE
Retrocopy HTMVKAAIDSRWTQPRETAEERKARLSEWKAGKGRVMKRPPSSVVTQPEPEAHNEKLVGSFWTTMAEEDE

Parental  QRVFTEKVNKTFSECLNLINEGCPKEEVLVTLNDLIKNIPDAKKLVKYWICLARVEPLTSPI-ENVIAIY
          QR.FT.KVNKTFSECL.LINEGCPKEEVLVTLNDLIKNIPDAKK.VKYWICLA..EPLTS...EN..AIY
Retrocopy QRLFTGKVNKTFSECLHLINEGCPKEEVLVTLNDLIKNIPDAKKHVKYWICLAHIEPLTSLL<ENIFAIY

Parental  EKAILAGAQPIEEMRHAIVDILTMKSQEKVKFGENIEEACATKEQIQEATTDDTSVNLGSEKPEIENKHP
          EKAILAGAQP.E.MRHAIVDILTMKSQEKVKFGENI.EACATKEQIQE.T.DD.SVNLGSEKPEIENKH.
Retrocopy EKAILAGAQPTEDMRHAIVDILTMKSQEKVKFGENI*EACATKEQIQENTIDDISVNLGSEKPEIENKHL

Parental  RNVVFQGCEKEQDDKTKDPTSDVKTPNTETRAGCLIKYNVSTTPYLQSVK-KKMQFDETNSAFKELKFLT
          RNVVFQGCEKEQDDKTKDPTSD.KTPNTETRAGCLIKYNVST.PYLQSVK.KKMQF..TNSAFKELK.LT
Retrocopy RNVVFQGCEKEQDDKTKDPTSDIKTPNTETRAGCLIKYNVSTSPYLQSVK<KKMQFNKTNSAFKELKILT

Parental  PVRRSRRLQEKTSKLPDMLKDHFPCVSSLEQLTELGSETDAFVCR
          PVR.S..LQEKTSKLPDMLKDH.PCVSSLEQLTELGSETDAFVCR
Retrocopy PVRHSQCLQEKTSKLPDMLKDHYPCVSSLEQLTELGSETDAFVCR

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_1741 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1741 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 ,