RetrogeneDB ID: retro_nleu_2402

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397352.1:7960883..7961677(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A3
• Ensembl ID: ENSNLEG00000005973
• Aliases: None
• Description: None

Sequence

>retro_nleu_2402
GCGGCGGCTGTGGAGGAGGCCAGCGTGGACTACGGCTCGGCCCGGTACCTGCTGCTGTGCGGCCTGGGCGGGATGCTGAG
CTGCGGCTGACACACACGGCCATCGTGTCCCTGGACCTGGTCAAGTGCCGCATGCAGGTGAACCCCGGCGGGTACAAGGG
CGTCCTCAGCGGCTTCGGCGTGACGGTGCGCAGCGACGGGCTGTGCAGTCTGGCTCGCGGCTGGGCCCAGACCTTCTTCG
GCTACTCCCTGCAGGGCTTCCTCAAGTTCGGCCTTTATGAGGTCTTCAAGATCCGCTACGCGGAGCTCCTGGGCCCAGAG
AAGGCCTACGGGTGGAGAACCGGCCTGTACCTTTTCGCCTGGGCTAGCGCCGAGTTCTTCGCCGACGTCTCGCTGGCGCC
CATGGAGGCGGTCAAGGTCCGCGTGCAGACGCGCCCGGGCTACGCCAGCACCCTGCGAGCCGCGGCGCCCAGGATGTAGG
GCGAGGAGGGCCTGTGGGCCTTCTACAGGGGCATGGCGCCGCTGTGGCTGAGGCAGATCTCCTACACCATGATGAAGTTT
GCCTGCTTCGAGCGCACGGCGGAGGAGCTCTACAGGTACGCCGTGCCCAAGCCCCAGAGCCAGTGCACCAAGGCCAAGCA
GCTGGGCATCACCTTCATGGCCAGCTACATCGCTGGCGTCTTCTGCGCTGTCGTGTCCCATCCCGCCGACTCTGTGGTGT
CTGTGCTGAACAAGGAGAAGGGCAGCACGGCCCTGGGCGTCCTCCGAAGACTGGGGTTCGCGGGCGTGGGGAAG

Alignment

ORF - retro_nleu_2402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.66 %
• Parental protein coverage: 73.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAAVEEQYSCDYGSGRFFILCGLGGIISCG-TTHTALVPLDLVKCRMQVDPQKYKGIFNGFSVTLKEDGV
          AAAVEE..S.DYGS.R...LCGLGG..SCG..THTA.V.LDLVKCRMQV.P..YKG...GF.VT...DG.
Retrocopy AAAVEEA-SVDYGSARYLLLCGLGGMLSCG<LTHTAIVSLDLVKCRMQVNPGGYKGVLSGFGVTVRSDGL

Parental  RGLAKGWAPTFLGYSMQGLCKFGFYEVFKVLYSNMLGEENTYLWRTSLYLAASASAEFFADIALAPMEAA
          ..LA.GWA.TF.GYS.QG..KFG.YEVFK..Y...LG.E..Y.WRT.LYL.A.ASAEFFAD..LAPMEA.
Retrocopy CSLARGWAQTFFGYSLQGFLKFGLYEVFKIRYAELLGPEKAYGWRTGLYLFAWASAEFFADVSLAPMEAV

Parental  KVRIQTQPGYANTLRDAAPKMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFERTVEALYKFVVPKPRSE
          KVR.QT.PGYA.TLR.AAP.M..EEGL.AFY.G.APLW.RQI.YTMMKFACFERT.E.LY...VPKP.S.
Retrocopy KVRVQTRPGYASTLRAAAPRM*GEEGLWAFYRGMAPLWLRQISYTMMKFACFERTAEELYRYAVPKPQSQ

Parental  CSKPEQLVVTFVAGYIAGVFCAIVSHPADSVVSVLNKEKGSSASQVLKRLGFKGVWK
          C.K..QL..TF.A.YIAGVFCA.VSHPADSVVSVLNKEKGS.A..VL.RLGF.GV.K
Retrocopy CTKAKQLGITFMASYIAGVFCAVVSHPADSVVSVLNKEKGSTALGVLRRLGFAGVGK

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_2402 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 27 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013232	1 retrocopy	retro_acar_35,
Bos taurus	ENSBTAG00000012890	1 retrocopy	retro_btau_172,
Canis familiaris	ENSCAFG00000006545	1 retrocopy	retro_cfam_880,
Callithrix jacchus	ENSCJAG00000002392	2 retrocopies	retro_cjac_3315, retro_cjac_812,
Dipodomys ordii	ENSDORG00000011431	1 retrocopy	retro_dord_321,
Equus caballus	ENSECAG00000015135	1 retrocopy	retro_ecab_481,
Echinops telfairi	ENSETEG00000012678	1 retrocopy	retro_etel_1748,
Homo sapiens	ENSG00000075415	1 retrocopy	retro_hsap_392,
Gorilla gorilla	ENSGGOG00000015886	1 retrocopy	retro_ggor_394,
Latimeria chalumnae	ENSLACG00000007024	1 retrocopy	retro_lcha_4,
Macropus eugenii	ENSMEUG00000016593	2 retrocopies	retro_meug_405, retro_meug_658,
Microcebus murinus	ENSMICG00000003520	1 retrocopy	retro_mmur_298,
Myotis lucifugus	ENSMLUG00000008330	1 retrocopy	retro_mluc_1184,
Macaca mulatta	ENSMMUG00000023036	1 retrocopy	retro_mmul_496,
Monodelphis domestica	ENSMODG00000007717	2 retrocopies	retro_mdom_2026, retro_mdom_293,
Mus musculus	ENSMUSG00000061904	1 retrocopy	retro_mmus_1959,
Nomascus leucogenys	ENSNLEG00000005973	1 retrocopy	retro_nleu_2402 ,
Oryctolagus cuniculus	ENSOCUG00000011847	1 retrocopy	retro_ocun_390,
Otolemur garnettii	ENSOGAG00000012222	2 retrocopies	retro_ogar_1816, retro_ogar_2052,
Pongo abelii	ENSPPYG00000004858	1 retrocopy	retro_pabe_1768,
Pan troglodytes	ENSPTRG00000005333	1 retrocopy	retro_ptro_302,
Pteropus vampyrus	ENSPVAG00000005890	1 retrocopy	retro_pvam_212,
Sorex araneus	ENSSARG00000001149	1 retrocopy	retro_sara_262,
Ictidomys tridecemlineatus	ENSSTOG00000027633	2 retrocopies	retro_itri_485, retro_itri_90,
Tupaia belangeri	ENSTBEG00000014548	1 retrocopy	retro_tbel_1792,
Tursiops truncatus	ENSTTRG00000004739	1 retrocopy	retro_ttru_692,
Vicugna pacos	ENSVPAG00000004704	1 retrocopy	retro_vpac_455,