RetrogeneDB ID: retro_ogar_411

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873521.1:8647572..8648170(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSOGAG00000012614
• Aliases: None
• Description: nuclear transcription factor Y, gamma [Source:HGNC Symbol;Acc:7806]

Sequence

>retro_ogar_411
TCTGTAACTGCCGCTGAGTCTGTCCAGTACTACTTCACGCTGGCTCAGCAGCCCACTGCCGTCCAAGTCCAGGGGCAGCA
GCAAGGCCAGCAGACTGCCAGCTCCACGGGCCACCATCCAGCCTGGGCAGATCATCATAGCACAGCCTCATCAGGGCCAG
ACCACACCTGTGACCATGCAAGTTAGAGAAGGTCAGCAGGTGCAGATTGTCTAGGCGCAGCGGCAGGCTCAAGCTCAACA
GGTCCAGAGTGGCAGTGGACAGACCATGCAGATGATGTAACAGATCATCATGAACACAGGGGAGATCCTGCAGATCCCAG
TACAGCTCAGTACTGGCCAGCTGCAGTGTGTCCACTTAGCCTAGCCTGTATCAGGCGCCCAAGTCGTGCAGGGACAGATC
CAGACACTTGCCACCAAGCCCAACAGATTACACAGACAGGGACAGCAAGAGCAGCAGCAGTTCAGCCAGTTCAGAGATGG
ACAGCAGCTCTACTAGATCCAGCAAGTCACCATGCCTGCCGGCCAGGACCTCACCCAGCCCATGTTCATCCAGTCAGCCA
ACCAGCCCTCTGACAGGCAGGTCCCTCAAGTGATAGGA

Alignment

ORF - retro_ogar_411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 59.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSST-TTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQI
          SVT.AE.VQYYFTLAQQPTAVQVQGQQQGQQT.SST..TIQPGQIIIAQP.QGQTTPVTMQV.EGQQVQI
Retrocopy SVTAAESVQYYFTLAQQPTAVQVQGQQQGQQTASST>ATIQPGQIIIAQPHQGQTTPVTMQVREGQQVQI

Parental  VQAQPQGQAQQAQSSSGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLAT-
          V.AQ.Q.QAQQ.QS.SGQTMQ.M.QII.NTGEI.QIPVQL..GQLQ...LA.PVSG.QVVQGQIQTLAT.
Retrocopy V*AQRQAQAQQVQSGSGQTMQMM*QIIMNTGEILQIPVQLSTGQLQCVHLA*PVSGAQVVQGQIQTLAT<

Parental  NAQQITQTEV-QQGQQQFSQFTDGQQLYQIQQVTMPAGQDLAQPMFIQSANQPSDGQAPQVTG
          .AQQITQT...Q..Q.QFSQF.DGQQLY.IQQVTMPAGQDL.QPMFIQSANQPSD.Q.PQV.G
Retrocopy QAQQITQTGT>QEQQ-QFSQFRDGQQLY*IQQVTMPAGQDLTQPMFIQSANQPSDRQVPQVIG

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_411 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012591	1 retrocopy	retro_acar_33,
Bos taurus	ENSBTAG00000021943	1 retrocopy	retro_btau_1338,
Callithrix jacchus	ENSCJAG00000002987	1 retrocopy	retro_cjac_4050,
Homo sapiens	ENSG00000066136	2 retrocopies	retro_hsap_4280, retro_hsap_4668,
Gorilla gorilla	ENSGGOG00000007360	2 retrocopies	retro_ggor_2865, retro_ggor_2896,
Macropus eugenii	ENSMEUG00000004480	1 retrocopy	retro_meug_1145,
Macaca mulatta	ENSMMUG00000014970	2 retrocopies	retro_mmul_1202, retro_mmul_2485,
Mus musculus	ENSMUSG00000032897	1 retrocopy	retro_mmus_844,
Otolemur garnettii	ENSOGAG00000012614	2 retrocopies	retro_ogar_2147, retro_ogar_411 ,
Pongo abelii	ENSPPYG00000001483	3 retrocopies	retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,
Pan troglodytes	ENSPTRG00000000596	2 retrocopies	retro_ptro_2903, retro_ptro_3102,