RetrogeneDB ID: retro_nleu_133

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: ADFV01135858.1:29313..30190(+)
• Located in intron of: ENSNLEG00000007788

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDOA
• Ensembl ID: ENSNLEG00000002152
• Aliases: None
• Description: Fructose-bisphosphate aldolase [Source:UniProtKB/TrEMBL;Acc:G1QQR3]

Sequence

>retro_nleu_133
ATGCCCTACCAATATCCAGCATTGACCCTGGAGCAGAAGAAGGAGCTGTCTGACATCGTTCCACCGCATCGTGGCACCGG
GCAAGGGCATCCTGGCTGCAGATGAGTCCACGGGAGCACTGCCAAGCAGCTGCAGTCCCTTGGCACCGAGAACACCGAAG
AGGACCGGCGCTTCTACCGCCAGCTGCTGCTGACAGCTGACGACTGCGTGAACCCCTGCACTGGGGACGTCATTCTCTTC
CACCAGACACTCTACCAGAAGAAGGATGATGGGCATCCCTTCCCCCAAGTTATCATAACCAAGGGCGGTGTTGTGGGCAT
CAAGGTAGACAAGGGCGTGGTCCCCCTCGCAGGGACAAATGGCGAGACCAGCCACCCAAGGGTTGTATGGGCTGTCTGAG
GGCTGTGCCCAGTACAAGAAGGATGGAGCTAACTTCGCCGAGTGGCATTGTGTTCTGAAGATTGGGGAACACACTCCCTC
AGCCTTTGCCATCATGGAAAATGCCAACGTCCTGGCCCGTTATGCCAGCATCTGCTAGCAGAATAGCACTGTGCCTGTTG
CGGTGCCTGAGATCCTCCCTGATGGGCACCATGACTTGAAGCGCTGCCAGTATGTGACCGAGAAGGTGCTGACTGCTGTC
TACAAGGCTCTGAGTGATCAACATATCTACCTGGAAGGCACCTTGCTGAACCCCAACATGGTCACCCCAGGCCATGCCTG
CACCCAGAAATTTTCTCACGAGGAAATTGCCATGGCGACTGTCACAACGCTGTGCCGCACAGTGCCCCCCGCTTTCCCTG
GGATCACCTTCCTGTCTGGAGGCCAGAGTGAGGAGGAGGCATCCATCAACCTGAATGCCATTAACAAGTGCCCCCTG

Alignment

ORF - retro_nleu_133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.78 %
• Parental protein coverage: 80.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPYQYPALTPEQKKELSDIA-HRIVAPGKGILAADESTGSI-AKRLQSIGTENTEENRRFYRQLLLTADD
          MPYQYPALT.EQKKELSDI..HRIVAPGKGILAADESTG...AK.LQS.GTENTEE.RRFYRQLLLTADD
Retrocopy MPYQYPALTLEQKKELSDIV>HRIVAPGKGILAADESTGAL<AKQLQSLGTENTEEDRRFYRQLLLTADD

Parental  RVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETT-TQGLDGLSERCAQ
          .VNPC.G.VILFH.TLYQK.DDG.PFPQVI..KGGVVGIKVDKGVVPLAGTNGET..TQGL.GLSE.CAQ
Retrocopy CVNPCTGDVILFHQTLYQKKDDGHPFPQVIITKGGVVGIKVDKGVVPLAGTNGETS>TQGLYGLSEGCAQ

Parental  YKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTE
          YKKDGA.FA.W.CVLKIGEHTPSA.AIMENANVLARYASIC.QN..VP...PEILPDG.HDLKRCQYVTE
Retrocopy YKKDGANFAEWHCVLKIGEHTPSAFAIMENANVLARYASIC*QNSTVPVAVPEILPDGHHDLKRCQYVTE

Parental  KVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVTGITFLSGGQSE
          KVL.AVYKALSD.HIYLEGTLL.PNMVTPGHACTQKFSHEEIAMATVT.L.RTVPPA..GITFLSGGQSE
Retrocopy KVLTAVYKALSDQHIYLEGTLLNPNMVTPGHACTQKFSHEEIAMATVTTLCRTVPPAFPGITFLSGGQSE

Parental  EEASINLNAINKCPL
          EEASINLNAINKCPL
Retrocopy EEASINLNAINKCPL

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_133 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 16 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008221	2 retrocopies	retro_cfam_190, retro_cfam_631,
Callithrix jacchus	ENSCJAG00000006874	1 retrocopy	retro_cjac_1803,
Cavia porcellus	ENSCPOG00000007434	1 retrocopy	retro_cpor_951,
Echinops telfairi	ENSETEG00000019230	1 retrocopy	retro_etel_20,
Homo sapiens	ENSG00000149925	1 retrocopy	retro_hsap_740,
Gorilla gorilla	ENSGGOG00000013979	1 retrocopy	retro_ggor_621,
Myotis lucifugus	ENSMLUG00000011210	3 retrocopies	retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta	ENSMMUG00000000983	1 retrocopy	retro_mmul_2596,
Monodelphis domestica	ENSMODG00000015696	4 retrocopies	retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus	ENSMUSG00000030695	3 retrocopies	retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys	ENSNLEG00000002152	1 retrocopy	retro_nleu_133 ,
Oryctolagus cuniculus	ENSOCUG00000006329	1 retrocopy	retro_ocun_1550,
Ochotona princeps	ENSOPRG00000009760	1 retrocopy	retro_opri_914,
Pongo abelii	ENSPPYG00000007244	1 retrocopy	retro_pabe_636,
Pan troglodytes	ENSPTRG00000007983	1 retrocopy	retro_ptro_526,
Rattus norvegicus	ENSRNOG00000023647	7 retrocopies	retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,