RetrogeneDB ID: retro_ogar_911

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873530.1:30617614..30618830(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC5
• Ensembl ID: ENSOGAG00000008296
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 5 [Source:HGNC Symbol;Acc:9552]

Sequence

>retro_ogar_911
ATGGCACTTGACAGGCTGGAGCAGACAGAGCTAAAAGAGGGGAAGGTAGGCAGTGGACTTCACCAATATTATCTGTCCAA
GATCGAAGAACTCCATCTGATTCTGAATGATAAGAGCCAAAACCTCTGCAGGCTGCAGACTCAAAGAAATGAATTAAATT
CAAAAGTTTGCCTATTGCAGTAGGAGCTACAGCTATTGTAAGAACAAGGCTCTTACATAGGGGAAGTAGTCCGAGCCGTG
GATAAGAAGAAAGTGTTGGTCAAGGTACATCCTGAGGGCAAGTTTGTCATAGATCTAGACAAAAAAATCGATATCAATGA
CCTGAAACCAAATTGCGGAGTGGCTCTGAGAAATGACAGCTACACTTTGCGCAAGATCCTACCCAACAAAGTGGACCCAC
TGGTATCACTGTTGATGGTGGAGAAGGTACCAGACTCGATTTACAAGATGATTGGTGGGCTGGACAAGCAGATCAAGGAG
ATCAAAGAACTGATTGAGCTGCCTTTTAAGCATCCTGAGCTCTCTGAAGCACTGGGCATCGCACAGCCCAAAGGAGTGCT
GCTGTATGGACCCCCTGGCACCTGGAAGATGTTGCTGGCCTGGGCTGTGGCTCATCATACAGACTGTACCTTCATTCATG
TGTCTGGCTCTGAGTTGGTACAGAAATTCATCAGGAAAGGGCAAGAATGGTGAGGGAGCTGTTTTTCATGGCATGAGAAC
ATGCTCCATCTATCATTTTCATGGATGAAATTGACTCCATTGGCTCCTCATGGCTGGAGGGGGATCTAGAGGGGACAGGG
AAGTGCAGCACACAGTACTGGAGCTGCTTAACCAGTTGGATGGCTTTGAGGCCACTAAGAATATCAAGGTTATAATGGCT
ACAAAAAAGATAGATATCTTGGATTAAGCCCTGCTTCGCCCAGGGTGTATTGACAGAAAAATTGAATTCCCACCCCCCAA
CGTGGAGGTCCAACTAGACATTCTGAAGATCCATTCTCGGAAAATGAACCTGACCCAGGGGATCAACCTGAAAAAAATTG
CTGAGCGCATGCCAAGAGCATCAGGGGCTGAAGTGAAGGGTGTGTGCATAGAAGCAGGCATGTATGCCACACGGGAACAG
CAAGTCCATGTCACCCAAGAAGACTTTGACATGGTGATAGCCAAGATCATGCAGAAGAATAGTGAGAAAAACATGTCCAT
CAAGAAACTATGGAAG

Alignment

ORF - retro_ogar_911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.07 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLREELQLLQEQG
          MALD..EQ.EL.EGK.GSGL.QYYLSKIEEL.LI.NDKSQNL.RLQ.QRNELN.KV.LL..ELQLL.EQG
Retrocopy MALDRLEQTELKEGKVGSGLHQYYLSKIEELHLILNDKSQNLCRLQTQRNELNSKVCLLQ*ELQLL*EQG

Parental  SYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDSYTLHKILPNKVDPLVSLMMV
          SY.GEVVRA.DKKKVLVKVHPEGKFV.D.DK.IDIND..PNC.VALRNDSYTL.KILPNKVDPLVSL.MV
Retrocopy SYIGEVVRAVDKKKVLVKVHPEGKFVIDLDKKIDINDLKPNCGVALRNDSYTLRKILPNKVDPLVSLLMV

Parental  EKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCT
          EKVPDS.Y.MIGGLDKQIKEIKE.IELP.KHPEL.EALGIAQPKGVLLYGPPGT.K.LLA.AVAHHTDCT
Retrocopy EKVPDSIYKMIGGLDKQIKEIKELIELPFKHPELSEALGIAQPKGVLLYGPPGTWKMLLAWAVAHHTDCT

Parental  FIRVSGSELVQKFIGEG-ARMVRELFVMAREHAPSIIFMDEIDSIGSSRLE-GGSGGDSEVQRTMLELLN
          FI.VSGSELVQKFI..G.ARMVRELF.MA.EHAPSIIFMDEIDSIGSS.LE.GGS.GD.EVQ.T.LELLN
Retrocopy FIHVSGSELVQKFIRKG<ARMVRELFFMA*EHAPSIIFMDEIDSIGSSWLE<GGSRGDREVQHTVLELLN

Parental  QLDGFEATKNIKVIMATNRIDILDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIA
          QLDGFEATKNIKVIMAT..IDILD.ALLRPG.IDRKIEFPPPN.E..LDILKIHSRKMNLT.GINL.KIA
Retrocopy QLDGFEATKNIKVIMATKKIDILD*ALLRPGCIDRKIEFPPPNVEVQLDILKIHSRKMNLTQGINLKKIA

Parental  ELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK
          E.MP.ASGAEVKGVC.EAGMYA.RE..VHVTQEDF.M..AK.MQK.SEKNMSIKKLWK
Retrocopy ERMPRASGAEVKGVCIEAGMYATREQQVHVTQEDFDMVIAKIMQKNSEKNMSIKKLWK

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_911 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002393	1 retrocopy	retro_dnov_1508,
Homo sapiens	ENSG00000087191	1 retrocopy	retro_hsap_1949,
Gorilla gorilla	ENSGGOG00000006803	1 retrocopy	retro_ggor_1418,
Macaca mulatta	ENSMMUG00000016769	1 retrocopy	retro_mmul_1354,
Monodelphis domestica	ENSMODG00000009873	2 retrocopies	retro_mdom_1411, retro_mdom_1583,
Nomascus leucogenys	ENSNLEG00000004150	1 retrocopy	retro_nleu_1480,
Oryctolagus cuniculus	ENSOCUG00000004329	1 retrocopy	retro_ocun_78,
Otolemur garnettii	ENSOGAG00000008296	1 retrocopy	retro_ogar_911 ,
Procavia capensis	ENSPCAG00000002653	1 retrocopy	retro_pcap_352,
Pongo abelii	ENSPPYG00000008533	1 retrocopy	retro_pabe_1606,
Pan troglodytes	ENSPTRG00000009525	1 retrocopy	retro_ptro_1303,
Ictidomys tridecemlineatus	ENSSTOG00000008945	1 retrocopy	retro_itri_1046,
Tupaia belangeri	ENSTBEG00000010546	3 retrocopies	retro_tbel_1411, retro_tbel_2422, retro_tbel_3450,
Tursiops truncatus	ENSTTRG00000006984	1 retrocopy	retro_ttru_1532,