RetrogeneDB ID: retro_ogar_1221

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873539.1:2671990..2672654(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSN
• Ensembl ID: ENSOGAG00000030436
• Aliases: None
• Description: translin [Source:HGNC Symbol;Acc:12379]

Sequence

>retro_ogar_1221
ATGTCTGTGAGCAAGATCTTGGTGGAGCTGCAGGGCTTTTGGCTGCCAAGCAGGATATCCAAGAGGCAATCTGAAAAGTT
GTAGAGTTTAGAACAAACAGCTTGTGAGATTTTAACTTTATTGCAAAGGTTCCATCAGGGGACTGGGTTTCAGGTCATTC
CAAAGAGGTGTGTGAAAGCTTGAGAACATTTGGTACACTAAAAACTCATCTAACATCTTTGAAGACCAAGTTCCCTGCTA
AACAAGATTACAGACTTCATCAACAGTGGAGGTTTGTGTCACAGCACTTGGTCATCTTGGCAGTATTTGTGTGCTTGAAA
ACAGCAATACTAGTGACTCAAGAAGCAGTTACAGAAATCCTTGGCATTGAGCCAGATCAGGAGAAAGGACTTCATCTGGA
TGTAGATTACCTCGCGGCAGTTCTCCTTCTTGCTCGTGGTGAACTGTCTGTTGACACTGTGACTGCTGGAGACTACTCTC
AGCTTCTCCACATCTCCACCTTCATCAGTGACCTGGATTCCAGTTTCCACCTTCTCAACCTGAAAAATTACTCCCTCAGG
AAGCCCTGTGATGGACTGAAGTATGACATGAAGACAGTAAGGAGGTGGCTTATGATCTCTCCATCTAGGGCTTCCATAAG
GATGTGGCGACAGCTTGGGTTGAA

Alignment

ORF - retro_ogar_1221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.69 %
• Parental protein coverage: 99.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREH-FGTVK
          MSVS.I.VELQGF............K...SLEQTA.EILTLLQ..HQG.GFQ.IPKRC.KA.EH.FGT.K
Retrocopy MSVSKILVELQGFWLPSRISKRQSEKL*-SLEQTACEILTLLQRFHQGTGFQVIPKRCVKA*EH<FGTLK

Parental  THLTSLKTKFPAEQYYRFHEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLDVED
          THLTSLKTKFPA.Q.YR.H..WRFV.Q.LV.LA.FV..L.T..LVT.EAVTEILGIEPD.EKG.HLDV.D
Retrocopy THLTSLKTKFPAKQDYRLHQQWRFVSQHLVILAVFVC-LKTAILVTQEAVTEILGIEPDQEKGLHLDV-D

Parental  YLSGVLILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKV-EEV
          YL..VL.LA.....LSV..VTAGDYS..LHISTFI..LDS.F.LLNLKN.SLRK..DGLKYD.K.V..EV
Retrocopy YLAAVLLLAR--GELSVDTVTAGDYSQLLHISTFISDLDSSFHLLNLKNYSLRKPCDGLKYDMKTV<KEV

Parental  VYDLSIRGFNKETAAACVE
          .YDLSI.GF.K..A.A.VE
Retrocopy AYDLSI*GFHKDVATAWVE

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_1221 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006059	1 retrocopy	retro_btau_1598,
Dasypus novemcinctus	ENSDNOG00000025740	2 retrocopies	retro_dnov_1581, retro_dnov_907,
Felis catus	ENSFCAG00000027149	1 retrocopy	retro_fcat_1577,
Homo sapiens	ENSG00000211460	1 retrocopy	retro_hsap_3760,
Gorilla gorilla	ENSGGOG00000002216	2 retrocopies	retro_ggor_2528, retro_ggor_2610,
Myotis lucifugus	ENSMLUG00000012656	1 retrocopy	retro_mluc_1420,
Macaca mulatta	ENSMMUG00000021119	1 retrocopy	retro_mmul_1718,
Monodelphis domestica	ENSMODG00000000147	1 retrocopy	retro_mdom_1896,
Nomascus leucogenys	ENSNLEG00000001202	1 retrocopy	retro_nleu_170,
Ornithorhynchus anatinus	ENSOANG00000003457	1 retrocopy	retro_oana_120,
Oryctolagus cuniculus	ENSOCUG00000023529	1 retrocopy	retro_ocun_271,
Otolemur garnettii	ENSOGAG00000030436	3 retrocopies	retro_ogar_1221 , retro_ogar_2875, retro_ogar_3426,
Pan troglodytes	ENSPTRG00000012420	1 retrocopy	retro_ptro_2551,
Tarsius syrichta	ENSTSYG00000004395	1 retrocopy	retro_tsyr_1593,