RetrogeneDB ID: retro_nleu_1967

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397319.1:14493811..14494496(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL45
• Ensembl ID: ENSNLEG00000000530
• Aliases: None
• Description: None

Sequence

>retro_nleu_1967
AACCTTCCCGGCAGCCTTTGCGTGAACAAAATGGCAACCCCCGTATCTCAGGGGTTGTCTCTTTTATTAAGGGTTTTGGG
CTGGTGATCTCGGCAGCCAGTTCTGGTGACTCAGTCTGCAGCTATAGTTCCAGTAAGAACTAAAAAAGGTTTCACACCTC
CTATTTATCAACCTAAATACAAAACACAAAAGGAGTTTATGGAACATGCCTGGAAAGCAGGACTGGTTATTCCTCCAGAA
CATCTGGATCGTCCCATACATCTGGCCTGTACAGCTGGTATCTTTGATGCCTATGTTCCTCCTGAGGGTGATGCTCACAT
GCCATCTCTTTCAAAGGAAGGACTGAAACAGAGAACTGAACAAATGAAGAAGAATGTGGCATACAATTGTCAGTCCAGAA
GATAAAAGAGTATCACGACAATTTTAAAACAAAGGACTTCCCTGAAAAAGCTAAGGATGTATTTACTGAAGCTCACCTTT
GTCTAAACAACTCACACATGACTGACTGCATACCTCGGTAACTGAACACTGTTTTCCAGACATGATCTGAGACATCAAAT
ATAAGACCATCCGCTGGAGCTTTGTGGAATCTTTAGAGCCCTACCATGTGGTTCAGGTTCGCTGTTCAAGTCTGACGAAC
CAGAGCAACATATACGGCTAGGTCACCATAGGCACACCCAGCAGA

Alignment

ORF - retro_nleu_1967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.76 %
• Parental protein coverage: 70.25 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLPGGLCGNKMAAPMPQVLSLLSRVLGWWSRQPVLVTQSAAIVPVRTKKRFTPPIYQPKFKTEKEFMQHA
          .LPG.LC.NKMA.P..Q.LSLL.RVLGW.SRQPVLVTQSAAIVPVRTKK.FTPPIYQPK.KT.KEFM.HA
Retrocopy NLPGSLCVNKMATPVSQGLSLLLRVLGW*SRQPVLVTQSAAIVPVRTKKGFTPPIYQPKYKTQKEFMEHA

Parental  RKAGLVIPPEKPDRSIHLACTAGIFDAYVPPEGDARISSLSKEGLIERTERMKKTMA-SQVSIRRIKDYD
          .KAGLVIPPE..DR.IHLACTAGIFDAYVPPEGDA...SLSKEGL..RTE.MKK..A..Q.S...IK.Y.
Retrocopy WKAGLVIPPEHLDRPIHLACTAGIFDAYVPPEGDAHMPSLSKEGLKQRTEQMKKNVA<IQLSVQKIKEYH

Parental  ANFKIKDFPEKAKDIFIEAHLCLNNQ-DHDRLHTLVTEHCFPDMTWDIKYKTVRWSFVESLEPSHVVQVR
          .NFK.KDFPEKAKD.F.EAHLCLNN...HD.LHT.VTEHCFPDM..DIKYKT.RWSFVESLEP.HVVQVR
Retrocopy DNFKTKDFPEKAKDVFTEAHLCLNNS<THD*LHTSVTEHCFPDMI*DIKYKTIRWSFVESLEPYHVVQVR

Parental  CSSMMNQGNMYGQVTVRMHTR
          CSS..NQ.N.YG.VT.....R
Retrocopy CSSLTNQSNIYG*VTIGTPSR

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_1967 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
Felis catus	ENSFCAG00000005808	2 retrocopies	retro_fcat_1677, retro_fcat_283,
Monodelphis domestica	ENSMODG00000012560	1 retrocopy	retro_mdom_403,
Nomascus leucogenys	ENSNLEG00000000530	1 retrocopy	retro_nleu_1967 ,
Otolemur garnettii	ENSOGAG00000015816	1 retrocopy	retro_ogar_1029,
Pan troglodytes	ENSPTRG00000009065	1 retrocopy	retro_ptro_107,
Ictidomys tridecemlineatus	ENSSTOG00000000304	2 retrocopies	retro_itri_102, retro_itri_1575,
Tupaia belangeri	ENSTBEG00000000585	1 retrocopy	retro_tbel_4621,
Vicugna pacos	ENSVPAG00000004977	1 retrocopy	retro_vpac_512,