RetrogeneDB ID: retro_nleu_387

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397264.1:16052544..16053542(+)
• Located in intron of: ENSNLEG00000017030

Retrocopy information

• Ensembl ID: ENSNLEG00000017034
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TM9SF3
• Ensembl ID: ENSNLEG00000013527
• Aliases: None
• Description: None

Sequence

>retro_nleu_387
AGTAAAGAGGAAGAAATGGATGATATGGATAGAGACCTAGGAAATGAATATGGATGGAAACAGGTGCATGGAGATGTATT
AGACCATCAAGTCACCGATATTTTCCTCTCTGATTGGTTCTGGATGTCAGATATTTGCTGTGTCTCTCATTGTTATTATT
GTTGCAATGATAGAAGATTTATATACTGACAGGGGATCAATGCTCAGTACAGCCGTATTTGTCTACGCTGCTACGTCTCC
AGTGAATGGTTATTTTGGAGGAAGTCTGTATGCTAGACAAGGAGGAAGGAGATGGATAAAGCAGATGTTTATTGGGGCAT
TCCTTATCCCAGCTATAGTGTGTGGCACTGCCTTCTTCATCAATTTCATAGCCATTTATTACCATGCTTCAAGAGCCATT
CCTTTTGGAACAATGGTGGCCGTTTGTTGCATCTGTTTTTTTGTTATTCTTCCTCTAAATCTTGTTGGTACAATACTTGG
CCGAAATCTGTCAGGTCAGCCCAACTTTCCTTGTCGTGTCAATGCTGTGCCTCGTCCTATATCAGAGAAAAAAATGGTTC
ATGGAGCCTGCGGTTATTGTTTGCCTGGGTGGAATTTTACCTTTTGGTTCAATCTTTATTGAAATGTATTTCATCTTCAC
GTCTTTCTGGGCATATAAGATATATTACGTCTATGGCTTCATGATGCTGGTGCTGGTTATCCTGTGCATTGTGACTGTCT
GTGTGACTATTGTGTGCACATATTTTCTACTAAATGCAGAAGATTACCGGTGGCAATGGACAAGTTTTCTCTCTGCTGCA
TCAACTGCAATCTATGTTTACATGTATTCCTTTTACTACTATTTTTTCAAAACAAAGATGTATGGCTTATTTCAAACATC
ATTTTACTTTGGATATATGGCAGTATTTAGCACAGCCTTGGGGATAATGTGTGGAGTGATTGGTTACATCGGAACAAGTG
TCTTTGTCCGAAAAATCTATACTAATGTGAAAATTGAC

Alignment

ORF - retro_nleu_387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.85 %
• Parental protein coverage: 60.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SKEEEMDDMDRDLGDEYGWKQVHGDV-FRPSSH-PLIFSSLIGSGCQIFAVSLIVIIVAMIEDLYTERGS
          SKEEEMDDMDRDLG.EYGWKQVHGDV..RPSSH.P..FSSLIGSGCQIFAVSLIVIIVAMIEDLYT.RGS
Retrocopy SKEEEMDDMDRDLGNEYGWKQVHGDV<IRPSSH<PI-FSSLIGSGCQIFAVSLIVIIVAMIEDLYTDRGS

Parental  MLSTAIFVYAATSPVNGYFGGSLYARQGGRRWIKQMFIGAFLIPAMVCGTAFFINFIAIYYHASRAIPFG
          MLSTA.FVYAATSPVNGYFGGSLYARQGGRRWIKQMFIGAFLIPA.VCGTAFFINFIAIYYHASRAIPFG
Retrocopy MLSTAVFVYAATSPVNGYFGGSLYARQGGRRWIKQMFIGAFLIPAIVCGTAFFINFIAIYYHASRAIPFG

Parental  TMVAVCCICFFVILPLNLVGTILGRNLSGQPNFPCRVNAVPRPIPE-KKWFMEPAVIVCLGGILPFGSIF
          TMVAVCCICFFVILPLNLVGTILGRNLSGQPNFPCRVNAVPRPI.E.KKWFMEPAVIVCLGGILPFGSIF
Retrocopy TMVAVCCICFFVILPLNLVGTILGRNLSGQPNFPCRVNAVPRPISE>KKWFMEPAVIVCLGGILPFGSIF

Parental  IEMYFIFTSFWAYKIYYVYGFMMLVLVILCIVTVCVTIVCTYFLLNAEDYRWQWTSFLSAASTAIYVYMY
          IEMYFIFTSFWAYKIYYVYGFMMLVLVILCIVTVCVTIVCTYFLLNAEDYRWQWTSFLSAASTAIYVYMY
Retrocopy IEMYFIFTSFWAYKIYYVYGFMMLVLVILCIVTVCVTIVCTYFLLNAEDYRWQWTSFLSAASTAIYVYMY

Parental  SFYYYFFKTKMYGLFQTSFYFGYMAVFSTALGIMCGAIGYMGTSAFVRKIYTNVKID
          SFYYYFFKTKMYGLFQTSFYFGYMAVFSTALGIMCG.IGY.GTS.FVRKIYTNVKID
Retrocopy SFYYYFFKTKMYGLFQTSFYFGYMAVFSTALGIMCGVIGYIGTSVFVRKIYTNVKID

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_387 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
Nomascus leucogenys	ENSNLEG00000013527	1 retrocopy	retro_nleu_387 ,
Nomascus leucogenys	ENSNLEG00000015344	1 retrocopy	retro_nleu_1965,
Tarsius syrichta	ENSTSYG00000000322	2 retrocopies	retro_tsyr_1760, retro_tsyr_1903,