RetrogeneDB ID: retro_nleu_1130

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:282642..283833(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3L
• Ensembl ID: ENSNLEG00000008850
• Aliases: None
• Description: None

Sequence

>retro_nleu_1130
CTGTCTCACTGGAAGTTCACTGTTCCCTGGCATGGGTCCCTAGGCTTCCTGCCTTGGAAGCACAGCAGCAGGCTTCATGG
GAAGGCGAAGAGCTTCCCTAAGGATGAACCTTCCAAGCCATTCCACCTCACAGCCTTCCTGGGATACAAGGCTGGTATGG
CCTACATCATGTGAGAAACTGACAGCCTAGGATCCAAGGCGAACAAGAAGGAAGTGGTAGAGGCTGTGACAGTTGTGGAG
ACACTGCCCATGGTAGTTGTGGGCATAGTGGCTATATGGAAACCCCTCAAGGCCTCCAGGCCTTCAAGACTGTCTTTGCT
GAGCACATCAGCAATGAATGCAAAGGTGCTTCTATAAGAACTGGCATAATCTATAAAGATGGCCTTTACCAAGTACTGCA
AGAAATGGCAGAATGAGGATGGCAACAAGCAGCTGGAGAAGGAATTCAACAGCATGAAAATGTACTGCCAAGTCATCTGT
ATCATTGCCCATACTCAGATGTGCCTGCTTCCTCTGTGCCAGAAGAAGGCACCCCGATGGAGATTGAGGTGAACTGAGGC
ACTGTGGCTGAGAAACTGGACTGGGCCCGGGAAATGCCAGAGCAGCAGATACCTGTGAACCAAATATTTGGGTAGGACAG
GGTAATTGATGCCATTGAGGTGACCAAGTGCAAAGGCTACAAAAGGGGTCACCAGTCATTGGCACACCAAGAAGCTGACC
CACAAGACCCACCAAAGGCTGTGTAAGGCTCCTTGTGTCAGGACGTGGCATCCTACCTGTGCGGCCTTCTCTGTGGCATG
TGCTGGGCAGAAAGGCTACCATCACTGCAGTGAGAATAACAAGATCTATAACATTGGCATGGCTACCTTATGAAGGACGA
AAAATGGATCAAGAACAATGCCTCCACTGATGATGACCTGTCTGACAAGAGCATCAACCCTCTGGGTGGCTTTGTCCACT
ATAATGAAGTGAACAATGACTTTGTCATGCTGAAAGGCTGTGTGGTGGGAATCAAGAAGTGAGTGCTCAGCTCCGCAAGC
CTTTGGTGGTGCAGTCTAAGCGTCCTGCTCTGAGAAGACTGACCTTAAGTTCATCAACACTGTTTCCAGGTTTGGCCCCT
TCCAGACCATGGAGGAGAAGAAAGCATTCATGGAACCACTAAAAAAGACCAGACTGCAAAGCAAGAGGGAG

Alignment

ORF - retro_nleu_1130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.05 %
• Parental protein coverage: 98.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGHLGFLPHKRSRRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKR
          .SH.KF..P.HG.LGFLP.K.S.R..GK.K..P.D.PS.P.HLTAFLGYKAGM.....E....G.K..K.
Retrocopy LSHWKFTVPWHGSLGFLPWKHSSRLHGKAKSFPKDEPSKPFHLTAFLGYKAGMAYIM*ETDSLGSKANKK

Parental  EEVEAVTIVETPPVVVVGVV-GYVATPRGLRSFKTIFAEHLSDECR-RRFYKDWHK-SKKKAFTKACKRW
          E.VEAVT.VET.P.VVVG.V.GY..TP.GL..FKT.FAEH.S.EC..R.FYK.WH..S.K.AFTK.CK.W
Retrocopy EVVEAVTVVETLPMVVVGIV<GYMETPQGLQAFKTVFAEHISNECK<RCFYKNWHN<SIKMAFTKYCKKW

Parental  RDTDGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKA-HIMEIQLNGGTVAEKVAWAQARLEKQVP
          ...DG.KQL.K.F..MK.YC.VI..I.HTQM.LLP..QKKA...MEI..N.GTVAEK..WA....E.Q.P
Retrocopy QNEDGNKQLEKEFNSMKMYCQVICIIAHTQMCLLPLCQKKA<TPMEIEVN*GTVAEKLDWAREMPEQQIP

Parental  VHSVFSQSEVIDVIAVTKGRG-VKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYH
          V...F....VID.I.VTK..G..KGVTS.WHTKKL..KTH..L.K..C...WHP.....S.A.AGQKGYH
Retrocopy VNQIFG*DRVIDAIEVTKCKG>TKGVTSHWHTKKLTHKTHQRLCKAPCVRTWHPTCAAFSVACAGQKGYH

Parental  HRTELNKKIYRIG-RGPHMEDGKLVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRV
          H..E.N.KIY.IG..G..M.D.K..KNNAST..D...KSI.PLGGF.HY.EVNNDFVMLKGC..G.KK.V
Retrocopy HCSE-NNKIYNIG<HGYLMKDEKWIKNNASTDDDLSDKSINPLGGFVHYNEVNNDFVMLKGCVVGIKK*V

Parental  IT-LRKSLLVHHSRQAV-ENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKKHLEKEKPE
          ...LRK.L.V...R.A..E...LKFI.T.S.F..G.FQT..EK.AFM.P.KK.....K.E
Retrocopy LS<LRKPLVVQSKRPAL<EKTDLKFINTVSRF--GPFQTMEEKKAFMEPLKKTRLQSKRE

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_1130 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 6 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008489	1 retrocopy	retro_amel_1881,
Nomascus leucogenys	ENSNLEG00000008850	9 retrocopies	retro_nleu_1107, retro_nleu_1130 , retro_nleu_1249, retro_nleu_1305, retro_nleu_1673, retro_nleu_1824, retro_nleu_2046, retro_nleu_2060, retro_nleu_3126,
Nomascus leucogenys	ENSNLEG00000015234	2 retrocopies	retro_nleu_1038, retro_nleu_1449,
Pongo abelii	ENSPPYG00000006973	1 retrocopy	retro_pabe_2854,
Pan troglodytes	ENSPTRG00000007617	12 retrocopies	retro_ptro_1439, retro_ptro_1473, retro_ptro_1753, retro_ptro_2150, retro_ptro_2339, retro_ptro_2462, retro_ptro_2501, retro_ptro_2646, retro_ptro_2741, retro_ptro_2767, retro_ptro_3163, retro_ptro_916,
Ictidomys tridecemlineatus	ENSSTOG00000012921	2 retrocopies	retro_itri_1344, retro_itri_867,