RetrogeneDB ID: retro_nleu_2712

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397405.1:2258324..2259129(+)
• Located in intron of: ENSNLEG00000011312

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFG
• Ensembl ID: ENSNLEG00000002849
• Aliases: None
• Description: None

Sequence

>retro_nleu_2712
ATGAATGGACAGTTGGACCTAAGCGGGAAGCTAATCATGAAAGCTCAACTTGGGGAGGATATTCCAAAAATTCCTATTCA
TAATGAAGATATTAATATTACTTATGATGAATTAGTGCTAATGATGCAAAGAGTTTTCAGGGGAAAGCTTCTGAGTAATG
TTGAAGTAACAATAAAGTATAAAGATGAAGATGACGATCTTCTAACAATTTTTGATAGTTCTGACCTTTCCTTTGCAATT
CAGTGTAGCAGGATACTGAAATTGACATTATTTGTTAATGGCCAACCAAGACCCCTTGAATCAAGTCAGGTGAAATATCT
CTGTCGAGAACTGACAGAACTTTGAAATAAAGTGAATCATTTATTGGACAGCTTGGAACCACCTGGAGAACCAGGACCTT
CCACCAATATTCCTGAAAATGTTACTGTGAATGGTAGGGAAGAAAAGCCTGCTTCTTCGGATTCTTCTGGAAAACAGTCT
ATTCAGGTTATGGCAGCAAGTATGTCAGCTTTTGACCCTTTAAAAAAACTAAGATGAAATAAAAAATAATGTTACGTCGG
CATTTGGCTTAACAGATGATCAGGTTTCAGGGCAACCCAGTGCTCCTGCAGAAGACTGTCCAGGAACATCTGACAGCATT
GCCGCCTCCTCCTCAGTAGCAGCTCACCCACCAGGAGTTCAGCCACGGCAACCACCATACACAGAAGCTAAGATACAAGC
AGATCAGACTGAAAGTCAGCTGTACCAACAGTACCAGCAACAGGCTAGCTATGACGTGCAGCTGTACCAACAGTACCAGC
AACAG

Alignment

ORF - retro_nleu_2712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.27 %
• Parental protein coverage: 66. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNGQLDLSGKLIIKAQLGEDIRRIPIHNEDI--TYDELVLMMQRVFRGKLLSNDEVTIKYKDEDGDLITI
          MNGQLDLSGKLI.KAQLGEDI..IPIHNEDI..TYDELVLMMQRVFRGKLLSN.EVTIKYKDED.DL.TI
Retrocopy MNGQLDLSGKLIMKAQLGEDIPKIPIHNEDINITYDELVLMMQRVFRGKLLSNVEVTIKYKDEDDDLLTI

Parental  FDSSDLSFAIQCSRILKLTLFVNGQPRPLESSQVKYLRRELIELRNKVNRLLDSLEPPGEPGPSTNIPES
          FDSSDLSFAIQCSRILKLTLFVNGQPRPLESSQVKYL.REL.EL.NKVN.LLDSLEPPGEPGPSTNIPE.
Retrocopy FDSSDLSFAIQCSRILKLTLFVNGQPRPLESSQVKYLCRELTEL*NKVNHLLDSLEPPGEPGPSTNIPEN

Parental  DTVDGREEKPA-SDSSGKQSTQVMAASMSAFDPL-KNQDEINKNVMSAFGLTDDQVSGPPSAPAEDRSGT
          .TV.GREEKPA.SDSSGKQS.QVMAASMSAFDPL.KN.DEI..NV.SAFGLTDDQVSG.PSAPAED..GT
Retrocopy VTVNGREEKPASSDSSGKQSIQVMAASMSAFDPL>KN*DEIKNNVTSAFGLTDDQVSGQPSAPAEDCPGT

Parental  PDSIASSSS-AAHPPGIQPQQPPYTGAQTQAGQIEGQMYQQYQQQAGYGAQQPQAPPQQ
          .DSIA.SSS.AAHPPG.QP.QPPYT.A..QA.Q.E.Q.YQQYQQQA.Y..Q..Q...QQ
Retrocopy SDSIAASSSVAAHPPGVQPRQPPYTEAKIQADQTESQLYQQYQQQASYDVQLYQQYQQQ

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_2712 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013928	1 retrocopy	retro_chof_406,
Homo sapiens	ENSG00000114354	1 retrocopy	retro_hsap_3459,
Macaca mulatta	ENSMMUG00000002863	1 retrocopy	retro_mmul_1760,
Nomascus leucogenys	ENSNLEG00000002849	1 retrocopy	retro_nleu_2712 ,
Ochotona princeps	ENSOPRG00000000781	3 retrocopies	retro_opri_34, retro_opri_849, retro_opri_958,
Pongo abelii	ENSPPYG00000013597	1 retrocopy	retro_pabe_2860,
Pan troglodytes	ENSPTRG00000015165	1 retrocopy	retro_ptro_2345,
Pteropus vampyrus	ENSPVAG00000017331	1 retrocopy	retro_pvam_1122,
Ictidomys tridecemlineatus	ENSSTOG00000025779	1 retrocopy	retro_itri_457,