RetrogeneDB ID: retro_nleu_2840

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397449.1:238624..239329(+)
• Located in intron of: ENSNLEG00000013978

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBLIM1
• Ensembl ID: ENSNLEG00000007650
• Aliases: None
• Description: None

Sequence

>retro_nleu_2840
GGATGTCCACCCCCTCCTTCTGTCCTGGATGGTTAGGACGTGCTTCCCCAACTGGACCTCCTCCCACCTGCTTCACCGTC
CCCTCCGGCGCTCCTGCCTTCTGAAGAGGAGGCTCCTGCTCCAATGGGGGCCTCACTTATTGCGGACTTAGAGCAGCTGC
ACCTGCCCCCATCCCCACCCCCACCACAGGCCCCTGCGGAGGGACCTTCAGTCCAGCCTGGGCCGGATCCCCTCAGGCCC
GTGGAAAAAGCTGCCGCCTCCCCCAGCAGAGCCTGTTGAGAGAGAGGCGTCCACAGACATCCGTGCCTTCTGCCATAAGA
CTGTCTCCCCCCAGGAGCTGGCTGTGGAGGCCATGAAGAGGCAGTACCATGCCCAGTTCTTCACGTGCCGTACCTGCCAC
CGCCAGCTGGCTGGGCAGAGCTTCTACCAGAAGGATGCGCGACCCCTTTGCGAACCCTGCTGCCAGGACACGCTGCAGAA
GTGCAGCAAGTGTGGCGAGGTGGTCCGGGAGCACATCATCGGGCCCCGGGCCAGGCCTTCCACCCCTCCTGCTTCACGTG
TGTGACCTGCGCCCGGTGCGTCGGGGATGAGAGCTTTGCCCTGGGCAGCCAGAACGAGGTGTACTGCCTGGACGACTTCT
ACAGGAAATTTGCCCCCGTCTGCAGCATCTGTGAGAATCCCGTCATTCCTCGGGATGGGAAAGAT

Alignment

ORF - retro_nleu_2840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.5 %
• Parental protein coverage: 63.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GCPPPPPVLDGEDVLPDLDLLPPPPPPPPVLLPSEEEAPAPMGASLIADLEQLHLSPPPPLPPPQAPAEG
          GCPPPP.VLDG.DVLP.LDLLPP..P.PP.LLPSEEEAPAPMGASLIADLEQLHL.P.P..PPPQAPAEG
Retrocopy GCPPPPSVLDG*DVLPQLDLLPPASPSPPALLPSEEEAPAPMGASLIADLEQLHLPPSP--PPPQAPAEG

Parental  PSVQPG--PLRPVEEEL-PPPPAESVEKGASTDICAFCHKTVSPRELAVEAMKRQYHAQCFTCRTCRRQL
          PSVQPG..PLRPVE....PP.PAE.VE..ASTDI.AFCHKTVSP.ELAVEAMKRQYHAQ.FTCRTC.RQL
Retrocopy PSVQPGPDPLRPVEKAA>PP-PAEPVEREASTDIRAFCHKTVSPQELAVEAMKRQYHAQFFTCRTCHRQL

Parental  AGQSFYQKDGRPLCEPCYQDTLERCGKCGEVVRDHII-RALGQAFHPSCFTCVTCARCIGDESFALGXXE
          AGQSFYQKD.RPLCEPC.QDTL..C.KCGEVVR.HII.RA.GQAFHPSCFTCVTCARC.GDESFALG...
Retrocopy AGQSFYQKDARPLCEPCCQDTLQKCSKCGEVVREHII<RAPGQAFHPSCFTCVTCARCVGDESFALGSQN

Parental  RLPSMGSFASRKFAPVCSICENPIIPRDGKD
          .......F..RKFAPVCSICENP.IPRDGKD
Retrocopy EVYCLDDF-YRKFAPVCSICENPVIPRDGKD

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_2840 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018725	1 retrocopy	retro_btau_1013,
Nomascus leucogenys	ENSNLEG00000007650	2 retrocopies	retro_nleu_1265, retro_nleu_2840 ,
Pteropus vampyrus	ENSPVAG00000009000	1 retrocopy	retro_pvam_415,