RetrogeneDB ID: retro_ogar_2147

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873596.1:4088665..4089659(-)
• 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_2147
ATGTCCACAGAAGGATTTGGTGGTACTAGCAGCAGTGATGCCCAGCAGAGCCTGCTGTCCTTCTGCCCTTGTGTTATGGA
AGAAATCCGGAATTTAACAGTGAAAGATTTCCAAGTACAAGAACTCCCACTGGCTCCTATTAAGGTTATGAAACTGGATG
AAGATGTGAAAATGATCAGTGCAGAAGCCCCTGTGCTGTTTGCCAAGGCAGCCCAGAGTTTTATCACTGAGTTGACTCTT
TGAGCCTGGATTCATACAGAGGATAACAAGCAACGGACTCTACAGAGGAATGATATCGCCAGGGCAATTACAAAATTTGA
TCAGTTTGACCTTCTCATCGATATTGTTCCAAGAGATGAACTGAAACCACCCAAACGTCAGGAGGAGGTGCGCCAGTCTG
TAACTCCTGCTGAGCCTGTCCAGTACTACTTCACACCAGCTCAGCAGCCCACTGCCATCCAAGTCCAGGGGCAGCAGCAA
GGCCAGCAGACCACCAGCTCCACGACCACCATCCAGCCTGGGCAGATCATCATCGCACAGCCTCAGCAGGGCCAGACCAC
ACCTGTGACCATGCAAGTTGGAGGTCAGCAGGTGCAGATTGTCCAGGCCCAGCCTCAGGGTCAAGCTCCGCAGGCCCAGA
GTAGCAGTGGACAGACCATGCAGGTGATGTAACAGATCATCACAAACACAGGAGAGACCCAGCAGATCCCGGTACAGTTC
AGTGCTGGCCAGCTGCAGTATATCCGCTTAGCCCAGCCTGTCTCAGGCACCCAAGTCGTACAGGGACAGATCCAGACACT
TGCCACCAATGCCTAGCAGATTACACAGACAGAGGTCCAGCAAGGACAGCAGCAGTTCAGCCAGTTCACAGATGGACAGC
AGCTCTACCAGATCCAGCAAGTCACCATGCCTGTGGGCCAGGACCTCGCCCAGCCCATGTTCATCCAGTTAGCCAACCAG
CCCTCCGGGGCAGGCCCCTCAGGTGACCGGTGAT

Alignment

ORF - retro_ogar_2147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFA
          MSTEG.FGGTSSSDAQQSL.SF.P.VMEEIRNLTVKDF.VQELPLA.IK..MKLDEDVKMISAEAPVLFA
Retrocopy MSTEG-FGGTSSSDAQQSLLSFCPCVMEEIRNLTVKDFQVQELPLAPIK-VMKLDEDVKMISAEAPVLFA

Parental  KAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAE
          KAAQ.FITELTL.AWIHTEDNK.RTLQRNDIA.AITKFDQFD.LIDIVPRDELKPPKRQEEVRQSVTPAE
Retrocopy KAAQSFITELTL*AWIHTEDNKQRTLQRNDIARAITKFDQFDLLIDIVPRDELKPPKRQEEVRQSVTPAE

Parental  PVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQPQG
          PVQYYFT.AQQPTA.QVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVG.GQQVQIVQAQPQG
Retrocopy PVQYYFTPAQQPTAIQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVG-GQQVQIVQAQPQG

Parental  QAQQAQSSSGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQITQT
          QA.QAQSSSGQTMQVM.QIITNTGE.QQIPVQ..AGQLQYIRLAQPVSGTQVVQGQIQTLATNA.QITQT
Retrocopy QAPQAQSSSGQTMQVM*QIITNTGETQQIPVQFSAGQLQYIRLAQPVSGTQVVQGQIQTLATNA*QITQT

Parental  EVQQGQQQFSQFTDGQQLYQIQQVTMPAGQDLAQPMFIQSANQPSDGQAP-QVTGD
          EVQQGQQQFSQFTDGQQLYQIQQVTMP.GQDLAQPMFIQ.ANQPS.G..P.QVTGD
Retrocopy EVQQGQQQFSQFTDGQQLYQIQQVTMPVGQDLAQPMFIQLANQPS-GAGP>QVTGD

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_2147 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,