RetrogeneDB ID: retro_nleu_2460

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397358.1:7680762..7681223(+)
• Located in intron of: ENSNLEG00000005363

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL9
• Ensembl ID: ENSNLEG00000006109
• Aliases: None
• Description: None

Sequence

>retro_nleu_2460
CCACAGGGGGCCACATCCAATGTCGTCGTGATATTTGACCAGTTCCACGTCCAGGAGTTTAAGGAGGCTTTCAACATGAT
TGACCAGAACCATGATGGCTTCATTGACAAGGGGGACAGCACGACAAGCTGGCTTCACCGGGAAAGAACCCCAAGGATGA
ATACCTGCAGGACATGATGAGCGAGGCCTCACGGCCGATCAACTTCACCACTTCCCTCACCATGTTTGGGGAGAAGCTGA
ATGGAACAGACCCCCAGGATGTGATCCAAAACGCCTTCACCTGCTTCAACGAGGAATCCTCAGGTTTCCATCTCCAGGAG
CTGCTCACCACCATGGGTGACAGCTTCACAGATGAGGAAGTGGATGAGATGTACTGGGAGGCTCCCATTGATAAAAACGG
CAAGTTCAACTAGGTGGAGGTCACCTGCATCCTCAAACATGGTGCCAAGGGCAAAGATGAC

Alignment

ORF - retro_nleu_2460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.1 %
• Parental protein coverage: 74.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDL-HDMLASLGKNPTDEYLEGMMSEAPGPINF
          PQ.ATSNV...FDQ...QEFKEAFNMIDQN.DGFIDK.D..HD.LAS.GKNP.DEYL..MMSEA..PINF
Retrocopy PQGATSNVVVIFDQFHVQEFKEAFNMIDQNHDGFIDKGDS<HDKLASPGKNPKDEYLQDMMSEASRPINF

Parental  TMFLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHEDHLRELLTTMGDRFTDEEVDEMYREAPIDKKGN
          T..LTMFGEKLNGTDP.DVI.NAF.CF.EE.SGF....HL.ELLTTMGD.FTDEEVDEMY.EAPIDK.G.
Retrocopy TTSLTMFGEKLNGTDPQDVIQNAFTCFNEESSGF----HLQELLTTMGDSFTDEEVDEMYWEAPIDKNGK

Parental  FNYVEFTRILKHGAKDKDD
          FN.VE.T.ILKHGAK.KDD
Retrocopy FN*VEVTCILKHGAKGKDD

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_2460 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008540	3 retrocopies	retro_cfam_1384, retro_cfam_2066, retro_cfam_2071,
Callithrix jacchus	ENSCJAG00000012890	4 retrocopies	retro_cjac_3193, retro_cjac_3195, retro_cjac_3743, retro_cjac_637,
Equus caballus	ENSECAG00000007545	1 retrocopy	retro_ecab_923,
Homo sapiens	ENSG00000101335	1 retrocopy	retro_hsap_956,
Gorilla gorilla	ENSGGOG00000024477	1 retrocopy	retro_ggor_770,
Myotis lucifugus	ENSMLUG00000000207	2 retrocopies	retro_mluc_2534, retro_mluc_327,
Nomascus leucogenys	ENSNLEG00000006109	1 retrocopy	retro_nleu_2460 ,
Nomascus leucogenys	ENSNLEG00000006907	3 retrocopies	retro_nleu_1709, retro_nleu_1906, retro_nleu_2250,
Pongo abelii	ENSPPYG00000010971	1 retrocopy	retro_pabe_972,
Pan troglodytes	ENSPTRG00000013458	1 retrocopy	retro_ptro_662,