RetrogeneDB ID: retro_nleu_1806

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397310.1:10215384..10216119(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000011462
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPMT
• Ensembl ID: ENSNLEG00000001548
• Aliases: None
• Description: None

Sequence

>retro_nleu_1806
ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCCGATACTGAGGTACAGAAAAACCAAGTACTAACTCTGGA
AGAATGGCAAGACAAGTTGGTGAACGGCAACACTGCTTTTCGTCAGGAACAAGGACATCAACTATTAAAGAAGAATTTAG
ATACTTTTCTTAAAGGCGAGAGTCGACTGAGGGTATTTTTTCCTCTTTGCGGAAAAGTGGTTGGGATGAAATGGTTTGCA
GACCGGGGACACAGTGTAGTTGGTGTGGAAATCAGTGAACTTGGGATACGAGAATTTTTTACAGAGCAGAATCTTTCTTA
CTCAGAAGAACCAATCACCAAAATGCCTGAAACTAAAGTAGTTAAGAGTTCTTTGGGGAACATTTCATTGTACTGTTGCA
GTATTTTCTATCTTCCCAGGACAAATATTGGCAAATTTGACATGATTTAGGATAGAGGAGCATTAGTTGCCATTAATCCA
GGTGATCGCAAATGCTATGCAGATATAATGTTATCCCTCCTGGGAAAGAAGTTTCAATATCTCTTGTGTGTTCTTTCTTA
TGATCCAACTAAACATCCAGGTCCACCATTTTACGTTCCACATGCTGAAATTGAAAGGTTGTTTGGTAAAATATGCAATA
TACATTGTCTTGAGAAGGTTGATGCTTTTGAAGAATGACTTAAAAGTTGGGGAATTGACTATCTTTTTGAAAAGTTATAT
CTACTTACAGAAAAG

Alignment

ORF - retro_nleu_1806 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDGTRTSPDIEEYSDTEVQKNQVLTLEEWQDKWVNGNTAFHQQQGHQLLKKHLDTFLKGKSGLRIFFPLC
          MDGTRTS.DIEEYSDTEVQKNQVLTLEEWQDK.VNGNTAF.Q.QGHQLLKK.LDTFLKG.S.LR.FFPLC
Retrocopy MDGTRTSLDIEEYSDTEVQKNQVLTLEEWQDKLVNGNTAFRQEQGHQLLKKNLDTFLKGESRLRVFFPLC

Parental  GKAVEMKWFADRGHSVIGVEISELGIREFFTEQNLSYSEEPITEIPGTKVFKSSSGNISLYCCSIFDLPR
          GK.V.MKWFADRGHSV.GVEISELGIREFFTEQNLSYSEEPIT..P.TKV.KSS.GNISLYCCSIF.LPR
Retrocopy GKVVGMKWFADRGHSVVGVEISELGIREFFTEQNLSYSEEPITKMPETKVVKSSLGNISLYCCSIFYLPR

Parental  TNIGKFDMIWDRGALVAINPGDRKCYADIMLSLLGKKFQYLLCVLSYDPTKHPGPPFYVPHAEIERLFGK
          TNIGKFDMI.DRGALVAINPGDRKCYADIMLSLLGKKFQYLLCVLSYDPTKHPGPPFYVPHAEIERLFGK
Retrocopy TNIGKFDMI*DRGALVAINPGDRKCYADIMLSLLGKKFQYLLCVLSYDPTKHPGPPFYVPHAEIERLFGK

Parental  ICNICCLEKVDAFEERHKSWGIDYLFEKLYLLTEK
          ICNI.CLEKVDAFEE..KSWGIDYLFEKLYLLTEK
Retrocopy ICNIHCLEKVDAFEE*LKSWGIDYLFEKLYLLTEK

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_1806 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 14 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008676	27 retrocopies	retro_chof_1029, retro_chof_1047, retro_chof_1184, retro_chof_1209, retro_chof_1425, retro_chof_1451, retro_chof_1483, retro_chof_1498, retro_chof_168, retro_chof_1830, retro_chof_1946, retro_chof_195, retro_chof_2039, retro_chof_2203, retro_chof_2543, retro_chof_2562, retro_chof_2649, retro_chof_330, retro_chof_503, retro_chof_626, retro_chof_637, retro_chof_684, retro_chof_743, retro_chof_761, retro_chof_78, retro_chof_79, retro_chof_921,
Callithrix jacchus	ENSCJAG00000006906	2 retrocopies	retro_cjac_1617, retro_cjac_4192,
Cavia porcellus	ENSCPOG00000005295	1 retrocopy	retro_cpor_666,
Dasypus novemcinctus	ENSDNOG00000004842	1 retrocopy	retro_dnov_965,
Homo sapiens	ENSG00000137364	4 retrocopies	retro_hsap_1884, retro_hsap_2781, retro_hsap_4835, retro_hsap_4868,
Gorilla gorilla	ENSGGOG00000016155	4 retrocopies	retro_ggor_1381, retro_ggor_1938, retro_ggor_3014, retro_ggor_3041,
Loxodonta africana	ENSLAFG00000011632	1 retrocopy	retro_lafr_438,
Macaca mulatta	ENSMMUG00000016627	3 retrocopies	retro_mmul_1445, retro_mmul_2576, retro_mmul_2609,
Mus musculus	ENSMUSG00000021376	1 retrocopy	retro_mmus_2738,
Nomascus leucogenys	ENSNLEG00000001548	4 retrocopies	retro_nleu_1806 , retro_nleu_2001, retro_nleu_2710, retro_nleu_682,
Oryctolagus cuniculus	ENSOCUG00000003854	2 retrocopies	retro_ocun_1255, retro_ocun_1370,
Otolemur garnettii	ENSOGAG00000007738	2 retrocopies	retro_ogar_1972, retro_ogar_701,
Pongo abelii	ENSPPYG00000016263	4 retrocopies	retro_pabe_1563, retro_pabe_2235, retro_pabe_3758, retro_pabe_3786,
Pan troglodytes	ENSPTRG00000017756	5 retrocopies	retro_ptro_1265, retro_ptro_1882, retro_ptro_3217, retro_ptro_3218, retro_ptro_3243,