RetrogeneDB ID: retro_nleu_600

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397268.1:40804112..40804644(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPS2
• Ensembl ID: ENSNLEG00000009364
• Aliases: None
• Description: None

Sequence

>retro_nleu_600
ATGTCACCAGAGGAGACCGAAGGAACAAATTTTGACGCTGCAGGAGAAGCTGTGGGCCCGGCAGAAAGACAAGAACCAGC
TTTTTCTGCAGCTCAAGAAAGTTTCCATGAGGAAGAAAAACGGAGGCGAAAGGAACAGAGCGATCTGACCTTCTGACATC
CGCTGTGAGCCGGTGGAGCCCGATTATTCACGCGGGGACTCGCCTCCTCCTCGGCATGCAGGCAGCGCTGGAGGGCACGA
TCGCCCGGGCATTGTCATAGCAGCTGACCCAGCCAAGCAGATGTTCAGACCCCACGTGCTTACGACCCGGAAGTCCGTGG
GTTCAGCGGCGGCTTTTGCAGGGACCCCAGAGCAGGCAGCCTGGGCGGTGCCGCTGGGACTGCTCAGCCCCTACCTCAAT
GTGGGCCCACACAGCTAGCCTATGGCCCTAGTCGGCAGCTCAGAGCAGTTCAGTGCTCCCTGAGGTGCATTCAGGTCCCG
GCCACGACCTTATTTTCTGCTGGGCCACTTTGAGCACACCCACACAGGCTTC

Alignment

ORF - retro_nleu_600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.02 %
• Parental protein coverage: 56.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MSLEET-KEQILKLEEKLLALQEEKHQLFLQLKKV-LHEEEKRRRKEQSDLT-TLTSAAYQQSLTVHTGT
          MS.EET.KEQIL.L.EKL.A.Q..K.QLFLQLKKV..HEEEKRRRKEQSDLT..LTSA....S...H.GT
Retrocopy MSPEET>KEQILTLQEKLWARQKDKNQLFLQLKKV<FHEEEKRRRKEQSDLT<LLTSAVSRWSPIIHAGT

Parental  HLL-SMQ-GSPGGHNRPGTLMAADRAKQMFGPQVLTTRHYVGSAAAFAGTPEH-GQFQGSPGGAYGTAQP
          .LL..MQ.GS.GGH.RPG...AAD.AKQMF.P.VLTTR..VGSAAAFAGTPE..G...G..G....TAQP
Retrocopy RLLLGMQ<GSAGGHDRPGIVIAADPAKQMFRPHVLTTRKSVGSAAAFAGTPEQ<GSLGGAAG----TAQP

Parental  PPHYGPTQPAYSPSQQLRA-PSAFPAVQ-YLSQPQPQPYAVHGHFQPTQTGF
          .P..GPTQ.AY.PS.QLRA..S..P.V....S.P...PY...GHF..T.TGF
Retrocopy LPQCGPTQLAYGPSRQLRA<SSVLPEVH<FRSRP--RPYFLLGHFEHTHTGF

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_600 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016576	2 retrocopies	retro_amel_1236, retro_amel_362,
Equus caballus	ENSECAG00000010635	2 retrocopies	retro_ecab_124, retro_ecab_480,
Homo sapiens	ENSG00000132522	2 retrocopies	retro_hsap_2738, retro_hsap_4222,
Gorilla gorilla	ENSGGOG00000001672	1 retrocopy	retro_ggor_1907,
Macropus eugenii	ENSMEUG00000010645	2 retrocopies	retro_meug_1327, retro_meug_182,
Myotis lucifugus	ENSMLUG00000026169	1 retrocopy	retro_mluc_1045,
Mus musculus	ENSMUSG00000023170	1 retrocopy	retro_mmus_1476,
Nomascus leucogenys	ENSNLEG00000009364	2 retrocopies	retro_nleu_2477, retro_nleu_600 ,
Pan troglodytes	ENSPTRG00000023046	1 retrocopy	retro_ptro_1852,
Pteropus vampyrus	ENSPVAG00000005052	1 retrocopy	retro_pvam_35,
Sus scrofa	ENSSSCG00000017940	1 retrocopy	retro_sscr_742,