RetrogeneDB ID: retro_nleu_2283

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397341.1:6732979..6734414(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000013566
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NOL11
• Ensembl ID: ENSNLEG00000001436
• Aliases: None
• Description: None

Sequence

>retro_nleu_2283
ATGGCAGTGCTAGAGGAAGAATTCACGTTGTCTTCGGTAGTCCTGAGCGCGGGGCCTGAAGGACTCCTAGGCATGAAGCA
GAGTGACAAAACAGACCAGTTTCTAGTGACAGACAGCGGCAGAACCATGATCCTCTATAAGGTTTCTGATCAGAAACCCT
TAGGGAGCTGGTCAGTGAAACAGGGTCAAATTGTAACATGTCCAGCTGTGTGCAACTTTCAAACTGGAGAGTATATTGTT
GTACACGATAATAAGGTTTTAAGAATCTGGAATAATGAAGATGGAAACCTGGATAAAGTATTTAAAGCTACATTGTCAGC
TGAAGTATATAGGATACTTTCAGTGCAAGGGTCAGAACCCTTGGTGCTCTTCAAGGAAGGTGTTCGTGGTTTAGAGGCCT
TGCTTGCAGACCCCCAGCAGAAAATTGAAACTGTTATCTCTGATGACGTGATTAAATGGGCAAAGTTTTTCATAGTATTC
AAACATCCTGTTTTAATTTTTATTACTGAAAAACATGGAAATCACTTTGCTTATGTGCAAATGTTTAACTCACATTTCTT
AACCAAATATACACTCTTACTTGGACAAGACAAAAACTCTTTTATGGAGAGTTTTACTGAATCAGTAGATCAGAAATTCA
TCTCTTTGATGTCATTAAGCTCTGATGGTTGTATATATGAAACCTTGATACCAATACATCCAACTGACCCAGAAAAAAAT
CAGAGCTTAGTTAAATCACTGTTGCTCAAGGCTGTTGTGTCTGGTAACGCTTGAAATGGAGTTGCACTCACTGCCCTGGA
TCAGGATCACGTCACAGTCCTAGGAAGTCCACTAGCAGCTTCATAAGGAATGCCTCTCTGTATGGAACATAAAATTTCAA
ACACTACAGACTTCAGAAGAGTTACCACAAGGGACCAGTGGTCAACCCTGGTATTATGGGGAAAATTTGTTTATGCTACG
TGGAAAATCTCTAACTGTGATTCCATACAACTGTGAAGTGTCATCATTAGCAGGTGCTCATGGAAAACTCAAGCATAGTC
AAGATCCAGGAACTCATGTCGTGCCCCATTTTGTAAACTGGGAAACACCTCAGGGATGTGGACTTGGGTCCCAGAACTCA
GAGCAGTCAAGAAGAATTTTAAGGAGACGAAAAGTTGAAATGAGTTTACAGCCAGAGGTATCACCATCCAAACAACTTTT
GTCAACCATAATGAAAGATTCAGAGAAACACACTGAAGTAGAAGTATGGAAATTTTTGGCTCTGAAGCAGACCCCTGACT
TTCATACTGTCACTGGGGACACAGTAACAGGACTTCTGGAAAGGTGTAAAGCAGAACCATCATTTTATCCCCAGAACTGT
CTGATGCAGCATATCCAAATGCATGTGCTTTCTTACAGTTTGTGCCCTGACTTAATGGAGATTGCCTTAAAAAAG

Alignment

ORF - retro_nleu_2283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.23 %
• Parental protein coverage: 69.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALEEEFTLSSVVLSAGPEGLLGVEQSDKTDQFLVTDSGRTVILYKVSDQKPLGSWSVKQGQIITCPAV
          MA.LEEEFTLSSVVLSAGPEGLLG..QSDKTDQFLVTDSGRT.ILYKVSDQKPLGSWSVKQGQI.TCPAV
Retrocopy MAVLEEEFTLSSVVLSAGPEGLLGMKQSDKTDQFLVTDSGRTMILYKVSDQKPLGSWSVKQGQIVTCPAV

Parental  CNFQTGEYIVVHDNKVLRIWNNEDVNLDKVFKATLSAEVYRILSVQGTEPLVLFKEGAVRGLEALLADPQ
          CNFQTGEYIVVHDNKVLRIWNNED.NLDKVFKATLSAEVYRILSVQG.EPLVLFKEG.VRGLEALLADPQ
Retrocopy CNFQTGEYIVVHDNKVLRIWNNEDGNLDKVFKATLSAEVYRILSVQGSEPLVLFKEG-VRGLEALLADPQ

Parental  QKIETIISDEEVIKWTKFFLVFRHPVLIFITEKHENYFAYVQMFNSCILTKYTLLLGQDENSVIESFTAS
          QKIET.ISD..VIKW.KFF.VF.HPVLIFITEKH.N.FAYVQMFNS..LTKYTLLLGQD.NS..ESFT.S
Retrocopy QKIETVISDD-VIKWAKFFIVFKHPVLIFITEKHGNHFAYVQMFNSHFLTKYTLLLGQDKNSFMESFTES

Parental  VDRKFISLMSLSSDGCIYETLIPIRPTDPEKNQSLVRSLLLKAVVSGNARNGVALTALDQDHVAVLGSPL
          VD.KFISLMSLSSDGCIYETLIPI.PTDPEKNQSLV.SLLLKAVVSGNA.NGVALTALDQDHV.VLGSPL
Retrocopy VDQKFISLMSLSSDGCIYETLIPIHPTDPEKNQSLVKSLLLKAVVSGNA*NGVALTALDQDHVTVLGSPL

Parental  ESS-KECLSVWNIKFQTLQTSKELPQGTSGQLWYYGEHLFMLHGKSLTVIPYKCEVSSLAGALGKLKHSQ
          ..S.KECLSVWNIKFQTLQTS.ELPQGTSGQ.WYYGE.LFML.GKSLTVIPY.CEVSSLAGA.GKLKHSQ
Retrocopy AAS>KECLSVWNIKFQTLQTSEELPQGTSGQPWYYGENLFMLRGKSLTVIPYNCEVSSLAGAHGKLKHSQ

Parental  DPGTHVMPHFVNWETPQGCGLGFQNSEQSRRILRRRKIEVSLQPEVPPSKQLLSTIMKDSEKHIEVEVRK
          DPGTHV.PHFVNWETPQGCGLG.QNSEQSRRILRRRK.E.SLQPEV.PSKQLLSTIMKDSEKH.EVEV.K
Retrocopy DPGTHVVPHFVNWETPQGCGLGSQNSEQSRRILRRRKVEMSLQPEVSPSKQLLSTIMKDSEKHTEVEVWK

Parental  FLALKQTPDFHTVIGDTVTGLLERCKAEPSFYPRNCLMQLIQTHVLSYSLCPDLMEIALKK
          FLALKQTPDFHTV.GDTVTGLLERCKAEPSFYP.NCLMQ.IQ.HVLSYSLCPDLMEIALKK
Retrocopy FLALKQTPDFHTVTGDTVTGLLERCKAEPSFYPQNCLMQHIQMHVLSYSLCPDLMEIALKK

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_2283 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130935	1 retrocopy	retro_hsap_4772,
Nomascus leucogenys	ENSNLEG00000001436	1 retrocopy	retro_nleu_2283 ,
Pongo abelii	ENSPPYG00000008567	1 retrocopy	retro_pabe_3715,
Pan troglodytes	ENSPTRG00000009566	1 retrocopy	retro_ptro_3178,