RetrogeneDB ID: retro_nleu_618

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397268.1:23576720..23577558(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FHL1
• Ensembl ID: ENSNLEG00000002560
• Aliases: None
• Description: None

Sequence

>retro_nleu_618
ATGGCGGAGAAGTTTGACTGTCTCTACTTCAGGGACCCCTTGCAGAGGAAAAAGTATGTGCAGAAGGGTGACCACCACTG
CTGCCTGAAATGCTTTGACAGCTTCTGTGCCAACACCTGCATAGAATGCTGCAAGTCCATCCGTGTGGACTCCAAGGAGG
TGCACTATAAGAACTGCTTCTGGCATGACCCCTGCTTCCACTGTGCCAAGTGCCTTCACCCCTTGCCAATGAGACCTTTG
TGGCCAAGGACAACAAGATCCTGTCCAACAAGTTTGCCACTCAGGAGGACTCTCCCAAGTGTAAGGGGTGCTTCAAGGCC
TTTGTGGCAGGAGATCAAAAATGGAGTACAAGGGGACCATCTCGCACAAAGACTGCTTCGCCTATAGCAACTGCAAGCAA
GTCATGGGGACTGGAAGCTTCTTCTCTAAAGGGAAGGACTTCTACTGTGTGACTTGCCATGAGATCAAGTTTGCTAAGCA
TTGCGTAAAGTGCAACAAGGCCATCGCATCTTGGGGAGTCACTTACCAGGATGAGCCCTGGCATGCCGAGTGCTTTGTGT
GTGTTACCTGCTCTGAGATGCCGGCTGTGCAGCGTTTCACTGCTGTGGAGGACCAGTAATACTGTGTGGATTGCTACAAG
AACATTGTGGCCAAGAAGTGTGCTGGATGCAAGCACCCCATCACTGGGTTTGGTAAAGACTCCAGTGTGGTGGCCTATGA
AGGACAATCCTGGCACGACTGCTGCTTCCACTGCAAAAAATGCTCTGTGAATCTGGCCAACAAGCACTTTGTTTTCCGTG
AGGAGCAAGTATATTGCCTTGACAGTGCCAAAAAGTTG

Alignment

ORF - retro_nleu_618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEKFDCHYCRDPLQGKKYVQKDGHHCCLKCFDKFCANTCVECRKPIGADSKEVHYKNRFWHDTCFRCAK
          MAEKFDC.Y.RDPLQ.KKYVQK..HHCCLKCFD.FCANTC.EC.K.I..DSKEVHYKN.FWHD.CF.CAK
Retrocopy MAEKFDCLYFRDPLQRKKYVQKGDHHCCLKCFDSFCANTCIECCKSIRVDSKEVHYKNCFWHDPCFHCAK

Parental  CLHPL-ANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQN-VEYKGTVWHKDCFTCSNCKQVIGT
          CLHPL.ANETFVAKDNKIL.NK..T.EDSPKCKGCFKA.VAGDQ...EYKGT..HKDCF..SNCKQV.GT
Retrocopy CLHPL<ANETFVAKDNKILSNKFATQEDSPKCKGCFKAFVAGDQK<MEYKGTISHKDCFAYSNCKQVMGT

Parental  GSFFPKGEDFYCVTCHETKFAKHCVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYY
          GSFF.KG.DFYCVTCHE.KFAKHCVKCNKAI.S.G.TYQD.PWHA.CFVCVTCS...A.QRFTAVEDQ.Y
Retrocopy GSFFSKGKDFYCVTCHEIKFAKHCVKCNKAIASWGVTYQDEPWHAECFVCVTCSEMPAVQRFTAVEDQ*Y

Parental  CVDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAK
          CVDCYKN.VAKKCAGCK.PITGFGK.SSVVAYEGQSWHD.CFHCKKCSVNLANK.FVF..EQVYC.D.AK
Retrocopy CVDCYKNIVAKKCAGCKHPITGFGKDSSVVAYEGQSWHDCCFHCKKCSVNLANKHFVFREEQVYCLDSAK

Parental  KL
          KL
Retrocopy KL

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_618 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000014336	2 retrocopies	retro_mluc_311, retro_mluc_814,
Mus musculus	ENSMUSG00000023092	1 retrocopy	retro_mmus_51,
Nomascus leucogenys	ENSNLEG00000002560	1 retrocopy	retro_nleu_618 ,
Rattus norvegicus	ENSRNOG00000000875	1 retrocopy	retro_rnor_2514,