RetrogeneDB ID: retro_nleu_1717

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397306.1:11496468..11497405(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000010041
• Aliases: None
• Description: Adenosylhomocysteinase [Source:UniProtKB/TrEMBL;Acc:G1RG91]

Sequence

>retro_nleu_1717
ATGTCTCATTAACTACTCTATGAAGTTGCTGACGTTGGTTTGGCTGCCTGGGGATGCAAGGCCCTGGACTCTGAGGAGAA
CAAGAAGCCATGCCTGATGCACGTATAGGAGCTGTACTCAGCCTCCAAGCCACTGAAGGGTGCCCACATCACCGGCTGCC
TGCACATGACTGTGGAGACAGTCGTCCTCACTGAGACCCTCCTTGTCCTGGGTGCTGAAGTGCAGTGGTCCAGCTGCAAC
ATCTTCTCCACCCAGGACCATGCAGCAGCTGCCATTACCAAGGCTGGGATTCCAGTGAACGCCTGGAAGGGAGAAACAGA
GAAGTACCTTTGGTGCACCAAGCAGACACTGTACTTCAAGGACAAGCTCCTCAGCATGATTTTGGACATCACTGGGAACC
TCACCAACCTCACCCACACTAAGTACCCACAACTCCTGTTGGGCATCAGAGACATCTCCGAGGAGACCATGACTGAGGTC
CACAACCTATACAAGATGATGGCCAATGGGATCCTGAAGGTGTCCGCCATCAGTATTAATGATTCTGTCACCAAGAGCAA
GTTTGACAACCTCTATGGCTGCCACCAGTCCCTCCTAAGATGGCATCAAGTAGGCCATAGGTGTGATGATTGCCAGCAAG
GTAGCTGTGGTAGCGGGCTATGGTGATGTGGGCAAGGGCTGTGCCCAGGCCCTGCAGGGTTTCGGGGCTCACGTCATTAT
CACCGAGATCGACCCCATCAATGCACTGCAGGCTGCCATGCAGGGCTATGAGGGGACCACCATGGACAAGGCCTGTCAGG
AGGGCAACATCTTTGTCACACCACGGGCTGTGTTGACATCATCCTTGGCTAGCTGCCCAACAGGCACTTTTGAACAGATG
AAGGATGATGCCATCGTGTGTAACACTGCACACTCTGATGTGAAAATCGATGTCAGG

Alignment

ORF - retro_nleu_1717 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.11 %
• Parental protein coverage: 71.69 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSASKPLKGARIAGCLHMTVETAVLIETLVAL
          MS..L.Y.VAD.GLAAWG.KALD..EN..P.LM...E.YSASKPLKGA.I.GCLHMTVET.VL.ETL..L
Retrocopy MSH*LLYEVADVGLAAWGCKALDSEENKKPCLMHV*ELYSASKPLKGAHITGCLHMTVETVVLTETLLVL

Parental  GAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIH
          GAEVQWSSCNIFSTQDHAAAAI.KAGIPV.AWKGET.E.YLWC..QTLYFKD..L.MILD..G.LTNL.H
Retrocopy GAEVQWSSCNIFSTQDHAAAAITKAGIPVNAWKGET-EKYLWCTKQTLYFKDKLLSMILDITGNLTNLTH

Parental  TKYPQLLPGIRGISEETTTGVHNLYKMMANGILRVPAINVNDSVTKSKFDNLYGCRESLI-DGIKRATDV
          TKYPQLL.GIR.ISEET.T.VHNLYKMMANGIL.V.AI..NDSVTKSKFDNLYGC..SL..DGIK.A..V
Retrocopy TKYPQLLLGIRDISEETMTEVHNLYKMMANGILKVSAISINDSVTKSKFDNLYGCHQSLL>DGIK*AIGV

Parental  MIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVT-TTGC
          MIA.KVAVVAGYGDVGKGCAQAL.GFGA.VIITEIDPINALQAAM.GYE.TTMD.ACQEGNIFVT.TTGC
Retrocopy MIASKVAVVAGYGDVGKGCAQALQGFGAHVIITEIDPINALQAAMQGYEGTTMDKACQEGNIFVT<TTGC

Parental  VDIILG----RHF-EQMKDDAIVCNIGHFDVEIDVK
          VDIILG....RHF.EQMKDDAIVCN..H.DV.IDV.
Retrocopy VDIILG*LPNRHF>EQMKDDAIVCNTAHSDVKIDVR

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_1717 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 18 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018101	1 retrocopy	retro_btau_1140,
Canis familiaris	ENSCAFG00000007504	2 retrocopies	retro_cfam_1486, retro_cfam_552,
Callithrix jacchus	ENSCJAG00000018303	7 retrocopies	retro_cjac_1028, retro_cjac_1248, retro_cjac_1806, retro_cjac_2132, retro_cjac_2839, retro_cjac_3287, retro_cjac_480,
Echinops telfairi	ENSETEG00000002576	1 retrocopy	retro_etel_444,
Homo sapiens	ENSG00000101444	6 retrocopies	retro_hsap_1496, retro_hsap_2325, retro_hsap_2365, retro_hsap_4213, retro_hsap_571, retro_hsap_803,
Gorilla gorilla	ENSGGOG00000014694	5 retrocopies	retro_ggor_1148, retro_ggor_1795, retro_ggor_2822, retro_ggor_3087, retro_ggor_511,
Monodelphis domestica	ENSMODG00000002753	1 retrocopy	retro_mdom_1974,
Mus musculus	ENSMUSG00000027597	1 retrocopy	retro_mmus_197,
Nomascus leucogenys	ENSNLEG00000010041	4 retrocopies	retro_nleu_1717 , retro_nleu_2785, retro_nleu_40, retro_nleu_929,
Oryctolagus cuniculus	ENSOCUG00000008592	1 retrocopy	retro_ocun_1886,
Otolemur garnettii	ENSOGAG00000016787	3 retrocopies	retro_ogar_3223, retro_ogar_3401, retro_ogar_3402,
Pongo abelii	ENSPPYG00000010935	9 retrocopies	retro_pabe_1247, retro_pabe_1978, retro_pabe_2108, retro_pabe_2189, retro_pabe_3446, retro_pabe_647, retro_pabe_658, retro_pabe_665, retro_pabe_718,
Pan troglodytes	ENSPTRG00000013414	7 retrocopies	retro_ptro_1015, retro_ptro_1698, retro_ptro_1730, retro_ptro_2860, retro_ptro_3011, retro_ptro_559, retro_ptro_771,
Rattus norvegicus	ENSRNOG00000017777	7 retrocopies	retro_rnor_1142, retro_rnor_1820, retro_rnor_1903, retro_rnor_2120, retro_rnor_569, retro_rnor_647, retro_rnor_839,
Sus scrofa	ENSSSCG00000007278	1 retrocopy	retro_sscr_119,
Tarsius syrichta	ENSTSYG00000007163	3 retrocopies	retro_tsyr_1178, retro_tsyr_1529, retro_tsyr_1582,
Tursiops truncatus	ENSTTRG00000003632	1 retrocopy	retro_ttru_1666,
Xenopus tropicalis	ENSXETG00000019486	1 retrocopy	retro_xtro_62,