RetrogeneDB ID: retro_nleu_1491

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397296.1:17216826..17217750(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6AP2
• Ensembl ID: ENSNLEG00000001441
• Aliases: None
• Description: None

Sequence

>retro_nleu_1491
ATGACTGTGTTTGTCGTGCTCCTGCCGTTGGTGGCGGGTGTTTGAGGGAACGAGTTTAGTTCCTGGTCTGTTATTTTCAG
AAATGGAAATTGGTCTATACCAGGAGAGTGAATCCCAGACGTGGCTGCATTGTCCATGGCCTTCTCTGTGAAGGAAAACC
TTTCTTGGCCAAGACTTGCAGTAGGTGACCTATTTCATCGTCCTCGGGCTACCGTCATGGTGATGGTGAAGGGAGTGGAC
AAACTGGCTCTACCACCAGGCAGTGTCATTTCATACCCTTTGGAGAATGCAGTTCCTTTTGGTCTTGACAGTGTTGCAAA
TTCCATTCGCTCTTTATTGTCTGAGGAAACTCCTGTTGTTTTGCAGTTGGCTCGTAGTGAGGAAAGAGTGTATTTGGTAG
AGAAGGCAAACTCAGTGTTTGAAGACCTTTCAGTCACCTTAGGACAGCTCCATAATTACTTGTTTCAGGAAAACTCCATT
CTCAGTTCACTTCCCCTGAATTCTCTGAGTAGGAACAATGGAGTTGACCTGCTCTTTCTTTCTGAACTCCAAGTGCTACA
TGATATTTAAAGCTTGGTGTCTTGTCGTAAGCATCTAGCCAAGGATCATTCTCCTAATTTATATTCACTGGAGCTGGCAG
GTTTGGATGAAATTGGGAAGCATTACGGGGAAGACTGAACAATTCAGAGTTGCTTCTAAAATCCTGTTGACGCTCTGCAA
AAGTTTGCAGATAACATGTACAATATTTATGGCGGGAATGCAGTGGTAGAGTTAGTCACTATTAAGTCATTTGACACCTC
CCTTATGAAGAACACAAGGACTATCTTTGAGGCAAAATAAGTGAAGGACCCAGCAAGTCCCTATAACCTTGCATATAATT
TTGAATATTCAGTGATTTTCAAGATGATACTTTGGATAATGATT

Alignment

ORF - retro_nleu_1491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.02 %
• Parental protein coverage: 90. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVFVVLLALVAGVLGNEFSILKSPGSVVFRNGNWPIPGERIPDVAALSMGFSVKEDLSWPGLAVGNLFH
          M.VFVVLL.LVAGV.GNEF....S..SV.FRNGNW.IPGE.IPDVAALSM.FSVKE.LSWP.LAVG.LFH
Retrocopy MTVFVVLLPLVAGV*GNEF----SSWSVIFRNGNWSIPGE*IPDVAALSMAFSVKENLSWPRLAVGDLFH

Parental  RPRATVMVMVKGVNKLALPPGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKA
          RPRATVMVMVKGV.KLALPPGSVISYPLENAVPF.LDSVANSI.SL.SEETPVVLQLA.SEERVY.V.KA
Retrocopy RPRATVMVMVKGVDKLALPPGSVISYPLENAVPFGLDSVANSIRSLLSEETPVVLQLARSEERVYLVEKA

Parental  NSVFEDLSVTLRQLRNRLFQENSVLSSLPLNSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPD
          NSVFEDLSVTL.QL.N.LFQENS.LSSLPLNSLSRNN.VDLLFLSELQVLHDI.SL.S..KHLAKDHSP.
Retrocopy NSVFEDLSVTLGQLHNYLFQENSILSSLPLNSLSRNNGVDLLFLSELQVLHDI*SLVSCRKHLAKDHSPN

Parental  LYSLELAGLDEI-GKRYGEDSEQFRDASKIL-VDALQKFADDMYNLYGGNAVVELVTVKSFDTSLIRKTR
          LYSLELAGLDEI.G...G...EQFR.ASKIL.VDALQKFAD.MYN.YGGNAVVELVT.KSFDTSL...TR
Retrocopy LYSLELAGLDEI>GSITGK-TEQFRVASKIL<VDALQKFADNMYNIYGGNAVVELVTIKSFDTSLMKNTR

Parental  TILEAKQAKNPASPYNLAYKYNFEYSVVFNMVLWIMI
          TI.EAK..K.PASPYNLA..YNFEYSV.F.M.LWIMI
Retrocopy TIFEAK*VKDPASPYNLA--YNFEYSVIFKMILWIMI

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_1491 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006109	1 retrocopy	retro_dnov_2102,
Homo sapiens	ENSG00000182220	1 retrocopy	retro_hsap_280,
Gorilla gorilla	ENSGGOG00000000532	1 retrocopy	retro_ggor_323,
Myotis lucifugus	ENSMLUG00000001159	1 retrocopy	retro_mluc_1613,
Macaca mulatta	ENSMMUG00000012762	1 retrocopy	retro_mmul_561,
Nomascus leucogenys	ENSNLEG00000001441	1 retrocopy	retro_nleu_1491 ,
Pongo abelii	ENSPPYG00000020251	1 retrocopy	retro_pabe_389,
Pan troglodytes	ENSPTRG00000021803	1 retrocopy	retro_ptro_233,