RetrogeneDB ID: retro_nleu_2156

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397332.1:3912496..3913521(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAICS
• Ensembl ID: ENSNLEG00000008786
• Aliases: None
• Description: None

Sequence

>retro_nleu_2156
CAGACAGCTTTTGCTGCTCCCGAGTGTGAAATGATTCCAACTGAATGGGTTTGCAGAAGAATAGTAACTGATTCTTTTCT
CAAAAGAAATCGTGATGACAAGGAAGGATATAAGTTTTACCCACCTAAAGTGGAGATGTTTTTCAAGGATGATGCTGGTA
ATGACCCACAGTCATCTCAGGGACAGCTAATTGCTACAAAATTTTGCTTTGGTGAACTTCTCATAGGCCAAACTGAAGTG
GATATCATGTCATACTACATAGGCTCTTTTCTGAAATACTGGAGAAATCTTGGTTGCCCCAGAACTGTACACTGGTTGAT
ATGAAGATCAAATTTGGTGTTGATGTAACCCCCAAAGAAATTGTTCTTGCTGATGTTATTGATAATGATTCCTGGAGACT
CTGGCCTTCCGTAGATGGAAGCCAACAGAAAGACAAACAGCCTCATCAGGACCTCAAAGAAGTAATTCCTGAAGGGCTCA
AGATGGTAAAGAAAGAGTTAGAGTGGGTTGCAGAGAGAGAAGAGTTGCTTTTGAAATTAGAAAGTCCGTGCAGGATGGCA
GTATTGGTAGGCTCTACTTCTGATCTTGGCCGCTGTGAAAAAATCAAGAAGGCCTGTGGAAATCTTGGCATTCCATGAGA
ACTTCAAGTAACATCTGTGCATAAAGGACCAGATAAAACTGAGGATTAAAGCTGAGTGTGAAGGGGATGGCATTCCCACT
GTGTTTGTGGCAGTGGCAGGCAGAAGAAATGGTTTGGGACCAGTGACATCTGGGAATACTGCATATCCAGTTATCAGCTG
TCCTCCGCTCAAGCAGACTGGGGAGCTCAGGATGTGTGGTCTTCTCCTCGACTACCCAGCGGTCTCGGCTGCTCAACCAC
CCTTTCTCCAGAAGGATCAGCTCAGTTTGCTGCTCAGATATTTGGGTTAAACAACCACTTGCTGTGGAGCAGACCGCAAG
CAAGTGTTCTGAACACATGGATTTTCTTGAAGCAGGTTGACAAGGAAATCAGATAATGTAATTTA

Alignment

ORF - retro_nleu_2156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.81 %
• Parental protein coverage: 74.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ETAFIAPQCEMIPIEWVCRRIATGSFLKRNPGVKEGYKFYPPKVELFFKDDANNDPQWSEEQLIAAKFCF
          .TAF.AP.CEMIP.EWVCRRI.T.SFLKRN...KEGYKFYPPKVE.FFKDDA.NDPQ.S..QLIA.KFCF
Retrocopy QTAFAAPECEMIPTEWVCRRIVTDSFLKRNRDDKEGYKFYPPKVEMFFKDDAGNDPQSSQGQLIATKFCF

Parental  AGLVIGQTEVDIMSHATQAIF-EILEKSWLPQNCTLVDMKIEFGVDVTTKEIVLADVIDNDSWRLWPSGD
          ..L.IGQTEVDIMS........EILEKSWLPQNCTLVDMKI.FGVDVT.KEIVLADVIDNDSWRLWPS.D
Retrocopy GELLIGQTEVDIMSYYIGSFL<EILEKSWLPQNCTLVDMKIKFGVDVTPKEIVLADVIDNDSWRLWPSVD

Parental  RSQQKDKQSYRDLKEVTPEGLQMVKKNFEWVAERVELLLKSESQCRVVVLMGSTSDLGHCEKIKKACGNF
          .SQQKDKQ...DLKEV.PEGL.MVKK..EWVAER.ELLLK.ES.CR..VL.GSTSDLG.CEKIKKACGN.
Retrocopy GSQQKDKQPHQDLKEVIPEGLKMVKKELEWVAEREELLLKLESPCRMAVLVGSTSDLGRCEKIKKACGNL

Parental  GIPCELRVTSAHKGPDETL-RIKAEYEGDGIP-TVFVAVAGRSNGLGPVMSGNTAYPVISCPPL-TPDWG
          GIP.EL.VTS.HKGPD.T....K....G...P.TVFVAVAGR.NGLGPV.SGNTAYPVISCPPL...DWG
Retrocopy GIP*ELQVTSVHKGPDKTE<GLKLSVKGMAFP<TVFVAVAGRRNGLGPVTSGNTAYPVISCPPL<QADWG

Parental  AQDVWSSLRLPSGLGCSTILSPEGSAQFAAQIFGLNNHLVWSKLRASILNTWISLKQADKKIRECNL
          AQDVWSS.RLPSGLGCST.LSPEGSAQFAAQIFGLNNHL.WS...AS.LNTWI.LKQ.DK.IR.CNL
Retrocopy AQDVWSSPRLPSGLGCSTTLSPEGSAQFAAQIFGLNNHLLWSRPQASVLNTWIFLKQVDKEIR*CNL

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_2156 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 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010577	1 retrocopy	retro_btau_508,
Cavia porcellus	ENSCPOG00000010749	1 retrocopy	retro_cpor_969,
Dasypus novemcinctus	ENSDNOG00000013413	1 retrocopy	retro_dnov_284,
Echinops telfairi	ENSETEG00000015242	2 retrocopies	retro_etel_1918, retro_etel_341,
Homo sapiens	ENSG00000128050	3 retrocopies	retro_hsap_3802, retro_hsap_3915, retro_hsap_3927,
Gorilla gorilla	ENSGGOG00000024392	1 retrocopy	retro_ggor_2643,
Mus musculus	ENSMUSG00000029247	6 retrocopies	retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126, retro_mmus_653, retro_mmus_971,
Nomascus leucogenys	ENSNLEG00000008786	2 retrocopies	retro_nleu_1274, retro_nleu_2156 ,
Otolemur garnettii	ENSOGAG00000003575	2 retrocopies	retro_ogar_2138, retro_ogar_865,
Procavia capensis	ENSPCAG00000008531	1 retrocopy	retro_pcap_172,
Pan troglodytes	ENSPTRG00000016081	2 retrocopies	retro_ptro_2662, retro_ptro_2670,
Rattus norvegicus	ENSRNOG00000002101	3 retrocopies	retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri	ENSTBEG00000006751	1 retrocopy	retro_tbel_3697,
Tarsius syrichta	ENSTSYG00000010497	2 retrocopies	retro_tsyr_2170, retro_tsyr_329,
Drosophila melanogaster	FBgn0020513	1 retrocopy	retro_dmel_82,