RetrogeneDB ID: retro_nleu_1814

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397311.1:3139880..3140667(-)
• Located in intron of: ENSNLEG00000008561

Retrocopy information

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

Parental gene information

• Parental gene symbol: G3BP1
• Ensembl ID: ENSNLEG00000016470
• Aliases: None
• Description: GTPase activating protein (SH3 domain) binding protein 1 [Source:HGNC Symbol;Acc:30292]

Sequence

>retro_nleu_1814
ACTTTCTATGATCGGGCAGTTGTCAGTAATGACATGGAAGAACATTTAGAGGAGCCAGTTGCTGAACTGGAGCCTGATCC
TGAACCAGAACCAGAATAAGAATGTGTATCTGAAATCCAAGAGGAAAAGTCTGAGCTAGTATTAGAAGAAACTGCTCCTG
AGGATGCTCAGAAGAGTTCTTCTCCAGCACCTGCAGACATATCTCAGACAGTATGGGAAGACCTGAGGACATTTTCTTGG
GTATCTGAGACCAGTAACAACCTTCAACCCAGTGGAGCTGTTCCAGTTACTGGGATACCTCCTTATGTTGGTAAAGTACT
AGCTTCACAGCCCTGTACAGTCTAAGCCTGAATCTCAGATTCCACAACAGAGACCTCAAAGGGATCAAAGGATGTGAGAA
CAACGAATAAATATTCCTCCCCAAAAGGGACCCAGACCAATCTGTGAGACTGGTGAGCAAGGTGACATTGAACCCCAAAG
AATGGTGAGACACCCTGACAGTCATCAACTCTTCTTTGGCAACCTGCTTCATGAAGTGGACAAATCAGAGCTTAAAGATT
TCTTTCAAAATTATGGGAACGTGGTGGAGTTGCGTATTAACAGTGGTGGGAAATTACCCAGTTTTGGTTTTGTTGTGTTT
GATGATTCTGAGCCTGTTCAGAAGGTCCTTAGCAACAGGCCCATCATGTTCAGAGGTGAGGTCCGTCTGAATGTGGAAGA
GAAGAAGACTCGAGCTGCCAGGGAAGGGGACCGACGAGATGATTACCTTAGGGGACCTGGAGGCCCT

Alignment

ORF - retro_nleu_1814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.36 %
• Parental protein coverage: 59.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TFYDQAVVSNDMEEHLEEPVAEPEPDPEPEPEQEPVSEIQEEKPEPVLEETAPEDAQKSSSPAPADIGQT
          TFYD.AVVSNDMEEHLEEPVAE.EPDPEPEPE.E.VSEIQEEK.E.VLEETAPEDAQKSSSPAPADI.QT
Retrocopy TFYDRAVVSNDMEEHLEEPVAELEPDPEPEPE*ECVSEIQEEKSELVLEETAPEDAQKSSSPAPADISQT

Parental  VQEDLRTFSWASVTSKNLPPSGAVPVTGIPPH-VVKVPASQPRPESKPESQIPPQRPQRDQRVREQRINI
          V.EDLRTFSW.S.TS.NL.PSGAVPVTGIPP...VK.....P...SKPESQIP.QRPQRDQR..EQRINI
Retrocopy VWEDLRTFSWVSETSNNLQPSGAVPVTGIPPY>LVKY*LHSP-VQSKPESQIPQQRPQRDQRM*EQRINI

Parental  PPQRGPRPIREAGEQGDIEPRRMVRHPDSHQLFIGNLPHEVDKSELKDFFQSYGNVVELRINSGGKLPNF
          PPQ.GPRPI.E.GEQGDIEP.RMVRHPDSHQLF.GNL.HEVDKSELKDFFQ.YGNVVELRINSGGKLP.F
Retrocopy PPQKGPRPICETGEQGDIEPQRMVRHPDSHQLFFGNLLHEVDKSELKDFFQNYGNVVELRINSGGKLPSF

Parental  GFVVFDDSEPVQKVLSNRPIMFRGEVRLNVEEKKTRAAREGDRRDNRLRGPGGP
          GFVVFDDSEPVQKVLSNRPIMFRGEVRLNVEEKKTRAAREGDRRD..LRGPGGP
Retrocopy GFVVFDDSEPVQKVLSNRPIMFRGEVRLNVEEKKTRAAREGDRRDDYLRGPGGP

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_1814 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006626	2 retrocopies	retro_cpor_1119, retro_cpor_464,
Mus musculus	ENSMUSG00000018583	3 retrocopies	retro_mmus_1389, retro_mmus_3229, retro_mmus_3688,
Nomascus leucogenys	ENSNLEG00000016470	1 retrocopy	retro_nleu_1814 ,
Oryctolagus cuniculus	ENSOCUG00000022143	1 retrocopy	retro_ocun_1352,
Otolemur garnettii	ENSOGAG00000001726	2 retrocopies	retro_ogar_3156, retro_ogar_3183,
Rattus norvegicus	ENSRNOG00000013186	1 retrocopy	retro_rnor_1282,