RetrogeneDB ID: retro_nleu_2369

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397348.1:1055595..1056204(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSNLEG00000012195
• Aliases: None
• Description: None

Sequence

>retro_nleu_2369
ATGGGAATTACAAAATTTGATCAGTTAGACTTTCTCGTTGATGTTGCTTTGACAGATGAACTGAACTCTCCAAAGCATCA
GGAGGAGGTGTGCCAGTCTATAACTCCTGCCAAGCCCATCTAGGACTACTTCACACTGGCTTAGCAGCCCTCCACGGTCC
AAGTCTAGGGACAGCAGCAAGGCCAGGAGACCACCAGCTCTATGACCACCATCCAGCTTGGGCAGATCATCACGCAGCCT
CAGCAGGGCCAGATCATGCCCCTGACAGTGCAGGTTGGAGAAGGTAGGCAGGTGCAGATTGTCCAGGCCCAACCACAGGG
TCAAGCCTAAAAGTCCTAGAGTGACACTGGACAGACTATGCAAGTTATGCAACAGATTATTACTAAAACAGGAGAGATCC
AGCAGATCCCAGTGTAGCTGAAGTTGGGCCAGCTAGAATATATTCTCTTAGTCCAGCCTGTATCAGGTACTCAAGTCGTG
CAGGAACAGATATAGATGCTTGCCAGCAATGCCCAACAGATTACATAGACAGAGGTCCAGTAAGGACAGCGGCACTTCAA
CCAGGTCACAGATGGACACAAGCTCTACCAGATCCAGCAAGTCACCATT

Alignment

ORF - retro_nleu_2369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.04 %
• Parental protein coverage: 87.55 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTT
          M.ITKFDQ.DFL.D....DEL..PK.QEEV.QS.TPA.P...YFTLA.QP..VQV.GQQQGQ.TTSS.TT
Retrocopy MGITKFDQLDFLVDVALTDELNSPKHQEEVCQSITPAKPI*DYFTLA*QPSTVQV*GQQQGQETTSSMTT

Parental  IQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQPQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQ
          IQ.GQII..QPQQGQ..P.T.QVGEG.QVQIVQAQPQGQA....S.TGQTMQVMQQIIT.TGEIQQIPV.
Retrocopy IQLGQII-TQPQQGQIMPLTVQVGEGRQVQIVQAQPQGQA*KS*SDTGQTMQVMQQIITKTGEIQQIPV*

Parental  LNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQITQTEVQQGQQQFSQFTDGQQLYQIQQVTM
          L..GQL.YI.L.QPVSGTQVVQ.QI..LA.NAQQIT.TEVQ.GQ..F.Q.TDG..LYQIQQVT.
Retrocopy LKLGQLEYILLVQPVSGTQVVQEQI*MLASNAQQIT*TEVQ*GQRHFNQVTDGHKLYQIQQVTI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2369 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012591	1 retrocopy	retro_acar_33,
Callithrix jacchus	ENSCJAG00000002987	1 retrocopy	retro_cjac_4050,
Nomascus leucogenys	ENSNLEG00000001111	1 retrocopy	retro_nleu_670,
Nomascus leucogenys	ENSNLEG00000012195	2 retrocopies	retro_nleu_2369 , retro_nleu_2850,
Pongo abelii	ENSPPYG00000001483	3 retrocopies	retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,