RetrogeneDB ID: retro_nleu_5

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397343.1:7994197..7995706(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018874
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PIP5K1A
• Ensembl ID: ENSNLEG00000010130
• Aliases: None
• Description: None

Sequence

>retro_nleu_5
ATGGCGTTGGCCTCCTCCCAACCGTCGTTGGCGGTCGGTTTTTCATCCTTTGATCCCGGGGCCCCTTCCTGTACCGCGTC
CTCAGCATCTGGAATCAAGAGGCCCATGGCATCTGAGGTGCCTTATGCCTCTGGCGTGCCCATCAAGAAAACAGGCCATC
GAGGTGTTGATTCCTCAGGAGAGACAACATATAAAAAGACAACCTCATCGGCCTTGAAAGGTGCCATCCAGTTAGGCATT
ACTTACACTGTGGGGAGCCTGAGTACCAAACCAGAGCGTGATGTCCTCATGCAAGATTTCTACGTGGTGGAGAGTATCTT
CTTCCCCAGTGAAGGGAGCAACCTGACCCCTGCTCATCACTACAATGACTTTCGTTTCAAGACCTATGCGCCTGTTGCCT
TCCGCTACTTTCGGGAGCTATTTGGTATCCCGCCCGATGATTACTTGTGCTCCCTCTGCAGTGAGCCGCTGACTGAACTG
GGTAGCTCTGGAGCTAGTGGTTCCCTGTTCTATGTGTCCAGCGACGATGAATTCATTATTAAGACAGTCCAACATAAAGA
GGCGGAGTTTCTGCAGAAGCTGCTTCCAGGATACTACTTGAACCTCAACCAGAACCCTCAGACTTTGCTGCCTAAATTCT
ATGGACTGTACTGTGTGCAGGCAGCTGGCAAGAACATTCGCATTGTGGTGATGAACAATCTTTTACCAAGATCCGTCAAA
ATGCATATCAAATATGACCTCAAAGGCTCAACCTACAAACGCCGGGCTTCCCAGAAAGAACGAGAGAAGCCTCTTCCCAC
ATTTAAAGATCTAGACTTCTTACAAGACATCCCTGATGGTCTTTTTTTGGAGGCTGACATGTACAATGCTCTCTGTAAGA
CCCTGCAGCGTGACTGTTTGGTGCTGCAGAGTTTCAAGATAATGGACTATAGCCTCTTGCTGTCAATCCACAATATAGAT
CATGCACAACGAGAGCCCTTAAGCAGCGACACTGTTCAAGTGTCAGTTGACACTCAAAGACTGGCCCCCCAAAAGGCTCT
GTATTCCACAGCCATGGAATCCATCCAGGGAGAGGCTGGACTGGGCGATAGCATGGAGACCAATGACCATATAGGTGGCA
TCCCTGCTCAGAATAGTAAAGGGGAAAGGCTTCTGCTTTATATTGGCATCATTGACATCCTACAGTCTTACACGTTTCTT
AAGAAGTTGGAGCACTCTTGGAAAGCCGTGGTACATGACGGGGACACTGTCTCGGTGCATCGCCCAGGCTTCTATGCTGA
ACGGTTCCAACGCTTCATGTGCAACCCAGTATTTAAGAAGATCCCTTTGAAGCCTTCTCCTTCCAAAAAGTTTCGGTCTG
GCTCATCTTTCTCTCCGCACACGGGCTCCAGTGGCAACTCCTGCATTACTTACCAGCCATTGGTCTCTGGGGAACACAAG
GCACAAGTGACAACAAAGGCGGAAGTGGAGCCAGGTGTTCACCTTGGTCGTCCTGATGTTTTACCTCAG

Alignment

ORF - retro_nleu_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.49 %
• Parental protein coverage: 82.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSVPYASGMPIKKIGHRSVDSSGETTYKKTTSSALKGAIQLGITHTVGSLSTKPERDVLMQDFYVVESIF
          S.VPYASG.PIKK.GHR.VDSSGETTYKKTTSSALKGAIQLGIT.TVGSLSTKPERDVLMQDFYVVESIF
Retrocopy SEVPYASGVPIKKTGHRGVDSSGETTYKKTTSSALKGAIQLGITYTVGSLSTKPERDVLMQDFYVVESIF

Parental  FPSEGSNLTPAHHYNDFRFKTYAPVAFRYFRELFGIRPDDYLYSLCSEPLIELCSSGASGSLFYVSSDDE
          FPSEGSNLTPAHHYNDFRFKTYAPVAFRYFRELFGI.PDDYL.SLCSEPL.EL.SSGASGSLFYVSSDDE
Retrocopy FPSEGSNLTPAHHYNDFRFKTYAPVAFRYFRELFGIPPDDYLCSLCSEPLTELGSSGASGSLFYVSSDDE

Parental  FIIKTVQHKEAEFLQKLLPGYYMNLNQNPRTLLPKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHIKYDL
          FIIKTVQHKEAEFLQKLLPGYY.NLNQNP.TLLPKFYGLYCVQA.GKNIRIVVMNNLLPRSVKMHIKYDL
Retrocopy FIIKTVQHKEAEFLQKLLPGYYLNLNQNPQTLLPKFYGLYCVQAAGKNIRIVVMNNLLPRSVKMHIKYDL

Parental  KGSTYKRRASQKEREKPLPTFKDLDFLQDIPDGLFLDADMYNALCKTLQRDCLVLQSFKIMDYSLLMSIH
          KGSTYKRRASQKEREKPLPTFKDLDFLQDIPDGLFL.ADMYNALCKTLQRDCLVLQSFKIMDYSLL.SIH
Retrocopy KGSTYKRRASQKEREKPLPTFKDLDFLQDIPDGLFLEADMYNALCKTLQRDCLVLQSFKIMDYSLLLSIH

Parental  NIDHAQREPLSSET-QYSVDTRRPAPQKALYSTAMESIQGEARRGGTMETDDHMGGIPARNSKGERLLLY
          NIDHAQREPLSS.T.Q.SVDT.R.APQKALYSTAMESIQGEA..G..MET.DH.GGIPA.NSKGERLLLY
Retrocopy NIDHAQREPLSSDTVQVSVDTQRLAPQKALYSTAMESIQGEAGLGDSMETNDHIGGIPAQNSKGERLLLY

Parental  IGIIDILQSYRFVKKLEHSWKALVHDGDTVSVHRPGFYAERFQRFMCNTVFKKIPLKPSPSKKFRSGSSF
          IGIIDILQSY.F.KKLEHSWKA.VHDGDTVSVHRPGFYAERFQRFMCN.VFKKIPLKPSPSKKFRSGSSF
Retrocopy IGIIDILQSYTFLKKLEHSWKAVVHDGDTVSVHRPGFYAERFQRFMCNPVFKKIPLKPSPSKKFRSGSSF

Parental  SRRAGSSGNSCITYQPSVSGEHKAQVTTKAEVEPGIHLGRPDVLPQ
          S...GSSGNSCITYQP.VSGEHKAQVTTKAEVEPG.HLGRPDVLPQ
Retrocopy SPHTGSSGNSCITYQPLVSGEHKAQVTTKAEVEPGVHLGRPDVLPQ

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_5 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000143398	2 retrocopies	retro_hsap_3420, retro_hsap_716,
Macaca mulatta	ENSMMUG00000005228	1 retrocopy	retro_mmul_1748,
Nomascus leucogenys	ENSNLEG00000010130	2 retrocopies	retro_nleu_468, retro_nleu_5 ,
Otolemur garnettii	ENSOGAG00000002846	1 retrocopy	retro_ogar_1855,
Pongo abelii	ENSPPYG00000000872	4 retrocopies	retro_pabe_3037, retro_pabe_3112, retro_pabe_59, retro_pabe_619,
Pan troglodytes	ENSPTRG00000001282	2 retrocopies	retro_ptro_2324, retro_ptro_511,