RetrogeneDB ID: retro_ogar_2586

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873636.1:5423339..5424728(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM14A
• Ensembl ID: ENSOGAG00000002492
• Aliases: None
• Description: LSM14A, SCD6 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:24489]

Sequence

>retro_ogar_2586
ATGAGCAGGGTCACCCCCTACGTCGGTAGCAAGATCAGCCTCATCTCCAAGGCCGAGATCCGCTACCAGGGCATCCTCTA
CACCATAGACACCGAGAACTCCACCGTAGCCCTCGCCAAAGTTCGATCCTTTGGTACCGAGGACAGACCAACAGATCGTC
CTATACCACCTCGAGATGAAGTCTTTGAATACATTATTTTCCGTGGGAGTGATATTAAAGACCTCACTGTTTGTGAGCCA
CCAAAGCCACAGTGTTCTTTGCCTCAAGACCCTGCTATCGTTCAGTCTTCCCTAGGCTCATCTGCTTCTTCATTCCAATC
AGTGGGTTCGTATGGACCTTTTGGCAGGATGCCAACATACAGCCAATTCAGTCTGAGTTCATTAGTTGGGCAGCAGTTTG
GTGCTGTTGGTGTTGCTGGAAGCTCCTGGACCTCCTTTGGAACAGAAACATCAAACAGTGGCACCTTATCCCAATGCAGC
GCGGTGGGCTCCGCCTTTACACAGGATACAAGATCTCTAAAGACACAGTTATCTCAAGGTCGTTCAAGCCCTCAGTTAGA
CCCTTTGAGAAAAAGCCTAACTATGGAACAAGCAGTACAGACCACCTCGGCCCACTTACCTGCTCCAGCACCTATTGGGA
GAAGGGGCCCTGTATCAACCAGGCCTTTGCCATCTACCAGCCAAAAAGCAGTAGAGAATCAAGAGCACAGGCGAGCTGAA
GTACATAAAGTATCAAGACCAGAAAATGAGCAACTCAGAAATGATAACAAGAGACAAGTAGCTCCAGGTGTTCCTTCAGC
TCCAAGAAGAGGGCGTGGGGGTCATCGAGGTGGCAGGGGAAGATTTGGTATTCGGAGAGATGGTCCAATGAAATTTCAGA
AAGACTTTGACTTTGAAAGTGCAAATGCACTATTTAACAAGGAAGAGATTGACAGAGAGTTTCATAATAAACTTAAATTA
AAAGAAGATAAACTTGAGAAACAAGACAAGCCTGTAAATGGTGACGATAAAGGAGACTCAGGAGTTGATACCCAGAACAG
TGAAGGAAATGCTGATGAAGAAGATCCACTGGGACCCAACTGCTACTATGACAAAACCAAGTCCTTCTTTGATAATATTT
CCTGTGATGATAATAAAGAACGAAGACCAACATGGGCTGAAGAGAGGAGATTAAATGCAGAAACATTTGGAATCCCACTT
CGTCCAAACCGTGGCCGTGGCGGGTACAGAGGCAGAGGAGGTCTCGGTTTCCATGGTGGCAGAGGGCGTGGCGGTGGCAG
AGGTGGTACATTCACCACCCCTGGAGGATTTCATGGCGGATTCAGAGGAGATCATGGAGGCAGGGAGTTTGCAGAATTTT
AATATAGGAAAACCACAGCTTTTGGACCC

Alignment

ORF - retro_ogar_2586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGS
          MS..TPY.GSKISLISKAEIRY.GILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGS
Retrocopy MSRVTPYVGSKISLISKAEIRYQGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGS

Parental  DIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSASSFQSVGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVAP
          DIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSASSFQSVGSYGPFGRMPTYSQFS.SSLVGQQFGAVGV..
Retrocopy DIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSASSFQSVGSYGPFGRMPTYSQFSLSSLVGQQFGAVGV--

Parental  QAGSSLTSFGTETSNSGTLSQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQTASAHLP
          .AGSS.TSFGTETSNSGTLSQ.SAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKS.TMEQAVQT.SAHLP
Retrocopy -AGSSWTSFGTETSNSGTLSQCSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSLTMEQAVQTTSAHLP

Parental  APAPVGRRSPVSTRPLPSTSQKAVENQEHRRAEVHKVSRPENEQLRNDSKRQVAPGAPSVPRRGRGGHRG
          APAP.GRR.PVSTRPLPSTSQKAVENQEHRRAEVHKVSRPENEQLRND.KRQVAPG.PS.PRRGRGGHRG
Retrocopy APAPIGRRGPVSTRPLPSTSQKAVENQEHRRAEVHKVSRPENEQLRNDNKRQVAPGVPSAPRRGRGGHRG

Parental  GRGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQDKPVNGEDKGDSGVDTQNS
          GRGRFGIRRDGPMKF.KDFDFESANA.FNKEEIDREFHNKLKLKEDKLEKQDKPVNG.DKGDSGVDTQNS
Retrocopy GRGRFGIRRDGPMKFQKDFDFESANALFNKEEIDREFHNKLKLKEDKLEKQDKPVNGDDKGDSGVDTQNS

Parental  EGNAEEEDPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRGSLGF
          EGNA.EEDPLGPNCYYDKTKSFFDNISCDDN.ERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRG.LGF
Retrocopy EGNADEEDPLGPNCYYDKTKSFFDNISCDDNKERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRGGLGF

Parental  RGGRGRGGGRGGTFTTPRGFRGGFRGGRGGREFADFEYRKTTAFGP
          .GGRGRGGGRGGTFTTP.GF.GGFRG..GGREFA.F.YRKTTAFGP
Retrocopy HGGRGRGGGRGGTFTTPGGFHGGFRGDHGGREFAEF*YRKTTAFGP

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_2586 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Callithrix jacchus	ENSCJAG00000010360	5 retrocopies	retro_cjac_1582, retro_cjac_2625, retro_cjac_3201, retro_cjac_3327, retro_cjac_840,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586 , retro_ogar_67,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693, retro_pabe_2906,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,