RetrogeneDB ID: retro_nleu_2062

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397325.1:13551878..13552533(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB4A
• Ensembl ID: ENSNLEG00000014339
• Aliases: None
• Description: None

Sequence

>retro_nleu_2062
ATGTCTCAGACGGCCATGTCCGAAACCTACGATTTTTTGTTTAAGTTCTTGGTTATTGGAAATGCAGGAACTGGCAAATC
TTGCTTATTTCATCAGTTTATTGAAAAAAAAATTCAAAGATGACTCAAATCATACAATAGGAGTGGAATTTGGTTCAAAG
GTAACAAATGTTGGTGGTAAATATGTAAAGTTACAAATATGGGATACAGCAAGACAAGAACGATTCAGGTCTGTGAAGAG
AAGTTATTACCGAGGCGCGACCCGGGCTATCCTCGTCTATGCTATCACCAGCCGAGAAACCTACAATGCGCTTACTAATT
GGTTAACAGATGCCCAAATGCTAGCGAGCCAGAACACTGTGATCATCCATTGTGGAAACAAGAAGGACCTGGATGCACAT
CGTGAAGTTATCTTCTTAGAAGACTCCAGATTTGCTCAAGAAAATGAGCTGATGTTTTTGGAAACAAGTGCACTAACAGG
GGAGAATGTAGAAAAGGCTTTTGTACAGTGTGCAAGAAAAATACTTAACAAAATTGAATCAGGTGAGCTGGACCGAGAAA
GAATGGGTTCAGATATTCAGTACGGAGATGCTGCCTTGAGACAGCTGAGGTCACCGCGGCACGCACGGGCCCCGAGCGCT
CAGGAGTGTGGTTGT

Alignment

ORF - retro_nleu_2062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQTAMSETYDFLFKFLVIGNAGTGKSCLLHQFIEKK-FKDDSNHTIGVEFGSKIINVGGKYVKLQIWDT
          MSQTAMSETYDFLFKFLVIGNAGTGKSCL.HQFI....FKDDSNHTIGVEFGSK..NVGGKYVKLQIWDT
Retrocopy MSQTAMSETYDFLFKFLVIGNAGTGKSCLFHQFIXXX>FKDDSNHTIGVEFGSKVTNVGGKYVKLQIWDT

Parental  AGQERFRSVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDLDADREVTFL
          A.QERFRSV.RSYYRGA..A.LVY.ITSRETYNALTNWLTDA.MLASQN.VII.CGNKKDLDA.REV.FL
Retrocopy ARQERFRSVKRSYYRGATRAILVYAITSRETYNALTNWLTDAQMLASQNTVIIHCGNKKDLDAHREVIFL

Parental  EASRFAQENELMFLETSALTGENVEEAFVQCARKILNKIESGELDPERMGSGIQYGDAALRQLRSPRRAQ
          E.SRFAQENELMFLETSALTGENVE.AFVQCARKILNKIESGELD.ERMGS.IQYGDAALRQLRSPR.A.
Retrocopy EDSRFAQENELMFLETSALTGENVEKAFVQCARKILNKIESGELDRERMGSDIQYGDAALRQLRSPRHAR

Parental  APNAQECGC
          AP.AQECGC
Retrocopy APSAQECGC

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_2062 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013866	5 retrocopies	retro_chof_1017, retro_chof_1761, retro_chof_2377, retro_chof_64, retro_chof_703,
Echinops telfairi	ENSETEG00000018042	3 retrocopies	retro_etel_1163, retro_etel_122, retro_etel_681,
Macaca mulatta	ENSMMUG00000017720	1 retrocopy	retro_mmul_2336,
Nomascus leucogenys	ENSNLEG00000012853	1 retrocopy	retro_nleu_467,
Nomascus leucogenys	ENSNLEG00000014339	1 retrocopy	retro_nleu_2062 ,
Pongo abelii	ENSPPYG00000000128	1 retrocopy	retro_pabe_3321,