RetrogeneDB ID: retro_pabe_3715

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:150152529..150153936(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOL11
• Ensembl ID: ENSPPYG00000008567
• Aliases: None
• Description: nucleolar protein 11 [Source:RefSeq peptide;Acc:NP_001125582]

Sequence

>retro_pabe_3715
TTGCTTAAGGCTGTTGTGTCTGGTAACACTTGAAATGGAGTTACACTCACTGCGCTGGATCAGGATCACGTCACAGTCCT
GGGAAGTCCACTAGCAGCTTCTAAGGAATGCCTCTCTGTATGGAACATAAAATTTCAAACACTACAGACTTCAAAAGAGT
TACCACAAGGGACCAGTGGTCAACTCTGGTATTATGGGGAAAATTTGTTTATGCTATGTGGAAAATCTCTAACTGTGATT
CCATACAACTGTGAAGTGTCATCATTAGCAGGTGCTCATGGAAAACTCAAGCATAGTCAAGATCCAGGAACTCATGTCGT
GCCCCATTTTGTAAACTGGGAAACACCTCAAGGATGTGGACTTGGGTCCCAGAACTCAGAGCAGTCAAGAAGAATTTTAA
GGAGATGAAAAATTGAAGTGAGTTTACAGCCAGAGGTATCACCATCCAAACAACTTTTGTCAACCATAATGAAAGATTCA
GAGAAACACACTGAAGTAGAAGTATGGAAATTTTTGGCTCTGAAGCAGACCCCTGACTTTCATACTGTCAATGGGGACAC
AGTAACAGGACTTCTGGAAAGATGTAAAGCAGAACCATCATTTTATCCCCAGAACTGTCTGATGCAGCTTATCCAAATGC
ATGTGCTTTCTTACAGTTTGTGCCCTGACTTAATGGAGATTGCCTTAAAAAAGAAAGATGTACAGTTGTTACAACTCTGT
CTACAGCAGTTCCCTGACATTCCTGAATCAGTCACCTGTGCTTGCTTAAAAATTTTCTTGAGAATTGGTGATGACAGTCT
TCAAGAAACAGATGTCAGTATGGAGTCAGTTTTTGACTATAGTAATTCTGTACATGATGAGAAAATGGAAGAGCAAACTG
GAATTCTTCAAAATGGCTTCAATCCTGAAGAAGATAAATACAATAACTGTGATCAAGAGTTAAATAAAAAGCCCCAGGAC
AAAACCAAGGAGACCATTTCATGCTCTGTGATACCAAAAAGAGCAGCTCTACTTAATGCAATTCTTCATTCAGCATATAG
CGAAACATTTCTTCTGCCTCATTTGAAAAACATCCCAGCACAGCATATCACACTGTTTCTCAAGTATTTGTGTTTCCTTT
ATCTGAAGTGTAGCGAAAATGCTACTATGACTCTTCCTGGAATACACCCACCTACCTTGAACCAGATTATGGATTGGATA
TGTCTACTTCTGGATGCAAATTTTACTGTTGTAGTAATGATGCCAGAAGCAAAGAGGCTATTGATAAATCTTTACAAGCT
TGTAAAATCTCTGATATCTGTTTATTCCGAGCTCAACAAGATTGAAGTAAGTTTTTGGGAGCTACAGAAATTAAATCAAG
AAAAGAATAATAGAGGATTATATTCAATTGAGGTGCTGGAGCTCTTC

Alignment

ORF - retro_pabe_3715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.96 %
• Parental protein coverage: 65.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLKAVVSDNTQNGVALTALDQDHVAVLGSPLAASKECLSVWNIKFQTLQTSKELSQGTSGQVWYYGEHLF
          LLKAVVS.NT.NGV.LTALDQDHV.VLGSPLAASKECLSVWNIKFQTLQTSKEL.QGTSGQ.WYYGE.LF
Retrocopy LLKAVVSGNT*NGVTLTALDQDHVTVLGSPLAASKECLSVWNIKFQTLQTSKELPQGTSGQLWYYGENLF

Parental  MLHGKSLTVIPYKCEVSSLAGALGKLKHSQDPGTHVVPHFVNWETPQGCGLGFQNSEQSRRILRRRKIEV
          ML.GKSLTVIPY.CEVSSLAGA.GKLKHSQDPGTHVVPHFVNWETPQGCGLG.QNSEQSRRILRR.KIEV
Retrocopy MLCGKSLTVIPYNCEVSSLAGAHGKLKHSQDPGTHVVPHFVNWETPQGCGLGSQNSEQSRRILRR*KIEV

Parental  SLQPEVPPSKQLLSTIMKDSEKHIEVEVRKFLALKQTPDFHTVVGDTVTGLLERCKAEPSFYPRNCLMQL
          SLQPEV.PSKQLLSTIMKDSEKH.EVEV.KFLALKQTPDFHTV.GDTVTGLLERCKAEPSFYP.NCLMQL
Retrocopy SLQPEVSPSKQLLSTIMKDSEKHTEVEVWKFLALKQTPDFHTVNGDTVTGLLERCKAEPSFYPQNCLMQL

Parental  IQTHVLSYSLCPDLMEIALKKKDVQLLQLCLQQFPDIPESVTCACLKIFLSIGDDSLQETDVSMESVFDY
          IQ.HVLSYSLCPDLMEIALKKKDVQLLQLCLQQFPDIPESVTCACLKIFL.IGDDSLQETDVSMESVFDY
Retrocopy IQMHVLSYSLCPDLMEIALKKKDVQLLQLCLQQFPDIPESVTCACLKIFLRIGDDSLQETDVSMESVFDY

Parental  SNSVHDEKMEEQTEILQNGFNPEEDKCNNCDQELNKKPQDETKESTSCPVVQKRAALLNAILHSAFSETF
          SNSVHDEKMEEQT.ILQNGFNPEEDK.NNCDQELNKKPQD.TKE..SC.V..KRAALLNAILHSA.SETF
Retrocopy SNSVHDEKMEEQTGILQNGFNPEEDKYNNCDQELNKKPQDKTKETISCSVIPKRAALLNAILHSAYSETF

Parental  LLPHLKDIPAQHITLFLKYLYFLYLKCSENATMTLPGIHPPTLNQIMDWICLLLDANFTVVVMMPEAKRL
          LLPHLK.IPAQHITLFLKYL.FLYLKCSENATMTLPGIHPPTLNQIMDWICLLLDANFTVVVMMPEAKRL
Retrocopy LLPHLKNIPAQHITLFLKYLCFLYLKCSENATMTLPGIHPPTLNQIMDWICLLLDANFTVVVMMPEAKRL

Parental  LINLYKLVKSQITVYSELNKIEVSFRELQKLNQEKNNRGLYSIEVLELF
          LINLYKLVKS.I.VYSELNKIEVSF.ELQKLNQEKNNRGLYSIEVLELF
Retrocopy LINLYKLVKSLISVYSELNKIEVSFWELQKLNQEKNNRGLYSIEVLELF

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.11 RPM	7.52 RPM
SRP007412_cerebellum	0.00 RPM	20.06 RPM
SRP007412_heart	0.06 RPM	8.13 RPM
SRP007412_kidney	0.00 RPM	13.39 RPM
SRP007412_liver	0.03 RPM	14.20 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3715 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3715 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4772
Pan troglodytes	retro_ptro_3178

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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,