RetrogeneDB ID: retro_ogar_1743

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873563.1:5759932..5760992(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKAP2
• Ensembl ID: ENSOGAG00000008428
• Aliases: None
• Description: cytoskeleton associated protein 2 [Source:HGNC Symbol;Acc:1990]

Sequence

>retro_ogar_1743
GACAGGCCTGCTTTATCTTCTAATTCCAAACTGATAGAAAAGCCAAAATCCACTCACCAGCGAAGATACACTACAGCAAA
TGCAACTGTTGATAATAGATCACCTCGACCCAAAGAAACATCAGAAGAGAGAAAAGCTCGTCTGAGTGAATGGAAAACTT
GCAAAGGAAGAGTGCTGAGAAGGTCCCCTAACTCAGTGGTTACTCACTGTGAGCCTGAAGGACAAAATGAAAAACCAGGT
GGATCTTTCTGGACCACCGTGGTAGAAGAAGAGGAACAAAGATTACTTATTGATAAAGTAAATGATACATTTTCCGAATG
CCTCAACCTGATTGATAAGGGATGTCCTAAAGAAGAAATACCAGTCACACTCATTGACCTGATTAAAAAAATTCCAGATG
CCACAAAACTTGGTAAGTATTGGATATGTCTTGCACGCATTGAACCAATTACAAGTCCTATTGAAAATATTATTGCAATC
TGTGAGAAGGCCATTCTGGCAGGGGCTCAGCCTATTGAAGAGCTGCAACCCATAATTGTAGATATTCTAACAATGAAGAG
TCAAGAGAAAGTTAGTCTCAGAGAAAATATTGAGGCTTGTGCAACCAAGCAACAAATCCAAGAAATCGACTGTGAAGATA
AAGAGCCAGGAGAACCAGAGATGGAGAGTGAACATCATAGGAATGTGATATTTCAAGATTGTGAAGAAGGGCAAGATGAC
AATACAAAAGAGCCAGCTGATAAGGTTAAACCCCCAGTGCAGAAGCCAGGGCAAGTTGCTTAATTAAATATATTGTATCT
TCTACACGTACTTGCAAAGTGGAAAAAAGGTGCAATTTAACAAAACGGATTTAACATTTAAAGAACTGAAATTTTTAACA
CCAGTGAGACGTTCTTGATGTCTTCAAGAAAAAGCTTCTAAATTGCCAAATATGTTAAAAGACTGTTATCCTTGTATATC
TTCACTGGAACAGTTAACAGCATTGGAAAGTGAAAGTGATGCTTTTGTTTGCCGCCCTAACATAGCACTGTGTGGGATGT
ACTCCGAGACTGAAACAACT

Alignment

ORF - retro_ogar_1743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.11 %
• Parental protein coverage: 52.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DRPALSSNSKPIEKPKSTHQRRYTTANATVDHRAARPKETSEERKARLSEWKAGKGGRVLKGPPNSVVTH
          DRPALSSNSK.IEKPKSTHQRRYTTANATVD.R..RPKETSEERKARLSEWK..KG.RVL...PNSVVTH
Retrocopy DRPALSSNSKLIEKPKSTHQRRYTTANATVDNRSPRPKETSEERKARLSEWKTCKG-RVLRRSPNSVVTH

Parental  HEPEGQNNFSAPLFNFWSK--EDDNSECFYEHLS-TNSVFITDLDDRCPKEEILVTLNDLIKKIPDATKL
          .EPEGQN....P...FW....E.............T.S......D..CPKEEI.VTL.DLIKKIPDATKL
Retrocopy CEPEGQNE--KPGGSFWTTVVEEEEQRLLIDKVNDTFSECLNLIDKGCPKEEIPVTLIDLIKKIPDATKL

Parental  VKYWICLARIEPITSPIENIIAIYEKAILAGAQKIKPIEELQPIIVDILTMKSQEQVNLGENIEACATKQ
          .KYWICLARIEPITSPIENIIAI.EKAILAGAQ...PIEELQPIIVDILTMKSQE.V.L.ENIEACATKQ
Retrocopy GKYWICLARIEPITSPIENIIAICEKAILAGAQ---PIEELQPIIVDILTMKSQEKVSLRENIEACATKQ

Parental  QIQEINCEDTEPGKPETDSEHHRNVTFQDCEEGQDDNTKEPADNVK-TPSAEARASCLIKYIVSSTPS-L
          QIQEI.CED.EPG.PE..SEHHRNV.FQDCEEGQDDNTKEPAD.VK.TPSAEARASCLIKYIVSST...L
Retrocopy QIQEIDCEDKEPGEPEMESEHHRNVIFQDCEEGQDDNTKEPADKVK<TPSAEARASCLIKYIVSSTRT<L

Parental  QSGKKVQFDKTDLTFKELKFLTPVRRSRRLQEKASKLPDMLKDFYPCISSLEQLTALESETDAFVCRPNI
          QSGKKVQF.KTDLTFKELKFLTPVRRS..LQEKASKLP.MLKD.YPCISSLEQLTALESE.DAFVCRPNI
Retrocopy QSGKKVQFNKTDLTFKELKFLTPVRRS*CLQEKASKLPNMLKDCYPCISSLEQLTALESESDAFVCRPNI

Parental  ALCGMYSKTETT
          ALCGMYS.TETT
Retrocopy ALCGMYSETETT

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1743 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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,