RetrogeneDB ID: retro_nleu_659

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397269.1:3323258..3323907(-)
• Located in intron of: ENSNLEG00000002150

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLTA
• Ensembl ID: ENSNLEG00000003874
• Aliases: None
• Description: clathrin, light chain A [Source:HGNC Symbol;Acc:2090]

Sequence

>retro_nleu_659
ATGGCTGAGCGAGATCCATTCGGTGTCCCCGCTGGCACCCCTGGGGATCCTGTCCTGGGGAACGGAGTGGCTGGCGCCAG
TGAAGAAGACCCAGCTGCGGCCTTCTTGGCACAGCAAGAGAGCAAGACTACGGGTATCAAGAACAACAAGGTCGCCTTCG
ACATCCTGGATGGTGTCACCCCCAGGCCCCAGCCACAAGGTGAACAGCTGGGAGTCCAGGTGCTGTTGATGGAGTGATGA
TGGTGACTACTACCAGGAAAGTAATGGTCCAAGAGACAATTATGCAGCTATTTCACAAGTGGATCGATTCCAATCACAGC
CTGAAAATATCTGCAGATGGAAAGAAGAGAAAATGGAATGCTCAGAAGCCCTTGCTGCCTATTCTCAGAAGCAAGAAGCA
GAGTGGAAAGAAAAAGGGATAAATGAGCTAGCAGAGTGGTGTGCAAGACAAGACGAGCAGCTACAGAAAAGAAAGGCAAA
CAACAGGGCAGAAGATTTTGTAAATGACATTGACGAGTCATCCCCCAGCACTGGGTGGCAACAGGTGGCCTGGTTGTGTG
ACTATAACCCCAAGTCAGCAAGCAGGCCAAAGAGGTCTCCTGCATGCACTCAGTCCTCAACTCCCTCAAGCAGGCGACCC
CTGGTGCAC

Alignment

ORF - retro_nleu_659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAELDPFGAPASAPGGPALGNGVAGAGEEDPAAAFLAQQESEIAGIENDE-AFAILDGGAPGPQPHGEP-
          MAE.DPFG.PA..PG.P.LGNGVAGA.EEDPAAAFLAQQES...GI.N...AF.ILDG..P.PQP.GE..
Retrocopy MAERDPFGVPAGTPGDPVLGNGVAGASEEDPAAAFLAQQESKTTGIKNNKVAFDILDGVTPRPQPQGEQ<

Parental  PGGPDAVDGVM-NGEYYQESNGPTDSYAAISQVDRLQSEPESIRKWREEQMERLEALDANSRKQEAEWKE
          .G.P.AVDGVM..G.YYQESNGP.D.YAAISQVDR.QS.PE.I..W.EE.ME..EAL.A.S.KQEAEWKE
Retrocopy AGSPGAVDGVM<DGDYYQESNGPRDNYAAISQVDRFQSQPENICRWKEEKMECSEALAAYSQKQEAEWKE

Parental  KAIKELEEWYARQDEQLQKTKANNRAAEEAFVNDIDESSPGTEWERVARLCDFNPKS-SKQAKDVSRMRS
          K.I.EL.EW.ARQDEQLQK.KANNRA..E.FVNDIDESSP.T.W..VA.LCD.NPKS.SKQAK.VS.M.S
Retrocopy KGINELAEWCARQDEQLQKRKANNRA--EDFVNDIDESSPSTGWQQVAWLCDYNPKS<SKQAKEVSCMHS

Parental  VLISLKQA-PLVH
          VL.SLKQA.PLVH
Retrocopy VLNSLKQA>PLVH

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_659 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001137	1 retrocopy	retro_btau_327,
Homo sapiens	ENSG00000122705	2 retrocopies	retro_hsap_4022, retro_hsap_955,
Macropus eugenii	ENSMEUG00000010858	1 retrocopy	retro_meug_480,
Macaca mulatta	ENSMMUG00000006132	2 retrocopies	retro_mmul_2319, retro_mmul_785,
Monodelphis domestica	ENSMODG00000002610	1 retrocopy	retro_mdom_1148,
Nomascus leucogenys	ENSNLEG00000003874	1 retrocopy	retro_nleu_659 ,
Pongo abelii	ENSPPYG00000019069	1 retrocopy	retro_pabe_3300,
Pan troglodytes	ENSPTRG00000020930	1 retrocopy	retro_ptro_2727,