RetrogeneDB ID: retro_ogar_1734

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873563.1:9617597..9618680(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCE1
• Ensembl ID: ENSOGAG00000001652
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109]

Sequence

>retro_ogar_1734
ATATCAAAAAGACCATCTTATGCTCCACCTCCCACCCCAGCTCCTGCAACACAAATGCCCAGCACACCAGGGTTTGTGGG
ATACAATCCATACAGTCATGGCCTACAACAAATACAGACTGGGAGGAAACCCGGGCACCAACACCCTTGGTCACAGCATC
CTCTGGTATTACGATTCTAAAATCCCCAAGGCCACCAGATAAGCCACTGTTGCCCTACATGAGGTACAGCAGAAAGGTCT
GGGACCAAGTAAAGGCTTCTAACCCTGACCTAAAGTTGTGGGAGATTGGCAAGATTATTGGTGGCATGTGGCGAGATCTC
ACTGATGAAGAGAAACAAGAATATTTAAACGAATACCAAGCAGACAAGATAGAGTACGATGAATCTATGAAGGTCTATCA
TAATTCTCCCACGTACCTTGCTTACCTAAACGCAAAAAGTCGTGCAGAAGCTGCTTTAGAGGAAGAAAGTTGACAAAGAC
AGTCTCACATAGAGAAAGGGGAACCTTACATGAGCTTTCAGCCTGCTGAAGATCCAGATGATTATGATGATGGCTTTTCA
ACGAAGCATACAGCCACCGCCCGTTTCCAGAGAAACCACCGCCTCATTAGTGAAATCCTTAGTGAGAGGGCGGTGCCAGA
CGTCCGGTCAGTTGTCACAACAGTTAGGATGCAGGTCCTCAAACAACAAGTCCAATCTTTAATGGTTTATCAGCGAAAAC
TAGAAGCTGAACTTCTTCAAATAGAGGAACGACATCAAGAAAAGAAGAGGAAATTTATGGAAAGCACAGATTCATTTAAC
AATGAACTTAAAAGATTGTGCAGTCTGAAGGTAGAAGTGGATATGGAGAAGATCGCGCTGAGATTGTGCAGGCAGAGGAG
CAGGCCCGCAAGAGGCAGGAGGAGAGGGAGAAGCTGAGCAGGCCAAGCGCAGTCAAGAGCAGTGTCGTCCCCGAGGAGAG
AGCCAGCAGAATGGTGAAGAAGGCACATCAACTCCTGAGGACAAGGAGAGTGGGCAGAAAGGGGGCGAAAACATGGCTGA
GAAAGGAACCAGTGATAGCAACACCGGCTCAGAGAGCAACAGT

Alignment

ORF - retro_ogar_1734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.45 %
• Parental protein coverage: 88.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSKRPSYAPPPTPAPATQMPSTPGFVGYNPYSHLAYNNYRLGGNP-GTNS-RVTASSGITIPKPPKPPDK
          .SKRPSYAPPPTPAPATQMPSTPGFVGYNPYSH........G..P.GTN...VTASSGITI.K.P.PPDK
Retrocopy ISKRPSYAPPPTPAPATQMPSTPGFVGYNPYSH-GLQQIQTGRKP>GTNT>LVTASSGITILKSPRPPDK

Parental  PLMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHNSPA
          PL.PYMRYSRKVWDQVKASNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEY.A.KIEY.ESMK.YHNSP.
Retrocopy PLLPYMRYSRKVWDQVKASNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYQADKIEYDESMKVYHNSPT

Parental  YLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDPDDYDDGFSMKHTATARFQRNHRLISEILS
          YLAY.NAKSRAEAALEEES.QRQS..EKGEPYMS.QPAEDPDDYDDGFS.KHTATARFQRNHRLISEILS
Retrocopy YLAYLNAKSRAEAALEEES*QRQSHIEKGEPYMSFQPAEDPDDYDDGFSTKHTATARFQRNHRLISEILS

Parental  ESVVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSFNNELKRLCGLKV
          E..VPDVRSVVTT.RMQVLK.QVQSLMV.QRKLEAELLQIEERHQEKKRKF.ESTDSFNNELKRLC.LKV
Retrocopy ERAVPDVRSVVTTVRMQVLKQQVQSLMVYQRKLEAELLQIEERHQEKKRKFMESTDSFNNELKRLCSLKV

Parental  EVDMEKIA-AEIAQAEEQARKRQEEREKEAAEQAERSQSSIVPEE--EQAASKAEEKKDDENIPMETEET
          EVDMEKIA.AEI.QAEEQARKRQEEREK.....A....SS.VPEE.......KA...............T
Retrocopy EVDMEKIA<AEIVQAEEQARKRQEEREKLSRPSAVK--SSVVPEERASRMVKKAHQLLRTRRVGRKGAKT

Parental  HL-EETTESQQNGEEGTS
          .L.E..T.....G.E..S
Retrocopy WL<EKGTSDSNTGSESNS

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_1734 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 17 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013573	4 retrocopies	retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Homo sapiens	ENSG00000073584	5 retrocopies	retro_hsap_1195, retro_hsap_1304, retro_hsap_3623, retro_hsap_3947, retro_hsap_922,
Gorilla gorilla	ENSGGOG00000011803	2 retrocopies	retro_ggor_1020, retro_ggor_931,
Microcebus murinus	ENSMICG00000009821	4 retrocopies	retro_mmur_1408, retro_mmur_1592, retro_mmur_608, retro_mmur_928,
Myotis lucifugus	ENSMLUG00000004609	1 retrocopy	retro_mluc_1209,
Macaca mulatta	ENSMMUG00000004005	3 retrocopies	retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furo	ENSMPUG00000014660	4 retrocopies	retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Mus musculus	ENSMUSG00000037935	5 retrocopies	retro_mmus_1111, retro_mmus_1127, retro_mmus_2437, retro_mmus_2618, retro_mmus_3194,
Nomascus leucogenys	ENSNLEG00000001957	4 retrocopies	retro_nleu_1060, retro_nleu_2051, retro_nleu_2083, retro_nleu_286,
Oryctolagus cuniculus	ENSOCUG00000008981	1 retrocopy	retro_ocun_59,
Otolemur garnettii	ENSOGAG00000001652	7 retrocopies	retro_ogar_1734 , retro_ogar_2059, retro_ogar_3199, retro_ogar_402, retro_ogar_454, retro_ogar_682, retro_ogar_760,
Ochotona princeps	ENSOPRG00000000985	1 retrocopy	retro_opri_731,
Pongo abelii	ENSPPYG00000008456	4 retrocopies	retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Pan troglodytes	ENSPTRG00000022902	5 retrocopies	retro_ptro_2451, retro_ptro_2678, retro_ptro_3039, retro_ptro_639, retro_ptro_894,
Pteropus vampyrus	ENSPVAG00000011355	1 retrocopy	retro_pvam_237,
Rattus norvegicus	ENSRNOG00000010676	7 retrocopies	retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tupaia belangeri	ENSTBEG00000000770	10 retrocopies	retro_tbel_1246, retro_tbel_1554, retro_tbel_2208, retro_tbel_2955, retro_tbel_4035, retro_tbel_4629, retro_tbel_4656, retro_tbel_658, retro_tbel_821, retro_tbel_844,