RetrogeneDB ID: retro_nleu_2645

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397386.1:4783519..4784294(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP29
• Ensembl ID: ENSNLEG00000000108
• Aliases: None
• Description: Synaptosomal-associated protein [Source:UniProtKB/TrEMBL;Acc:G1QGU2]

Sequence

>retro_nleu_2645
ATGCCAGCTTACCCTAAAAGCTACAATCCGTTCGAGGACGACGGGGAGGACGAAGGCGCCCGGCCAGCCCCTTGGAGGGA
CGCCCGAGACCTCCCCGACGGGCCCGACGCGCCCGCAGACAGGCAGCAGTACTTGCAGCAGGAGGTCCTCCGCAGGGCTG
AGGCCACGGCCGCCAGCACCAGCAGGTCCCTGGCCCTCATGTACGAGTCCGAGAAGGTTGGGGTCGCCTCTTCCGAAGAG
CTCGCCCGTCAGCGAGGAGTCCTAGAGCGCACAGAGAAGATGGTGGACAAGATGGACCAAGATTCGAAGACCAGCCAGAA
ACACATCAATAGCATTAAGAGTGTGTTTGGGGGGCTTGTCAATTGCTTCAAATCCAAACCAGTAGAGACCCCACCCGAAC
AGAATGGCACCCTCGCCTCCCAGCCCAACAGCAGATTGAAAGAAGCCATAAGTACAAGTAAAGAACAGGAAGCAAAGTAC
CAGGCCAGCCACCCAAACCTTAGAAAGCTGGATGATACAGACCCTGTCCCCAGAGGGGCTGGTTCTGCCATGACTACCGA
TGCTTACCCAAAGAGCCTATCACCTTCGAGCCTATCACCAGAAGATCAACAGCAACCTAGATGAGCTGTCCATGGGACTG
GGCTGTCTGAAGGACATAGCCCTGGGGATGCAGACAGAAATTGAGGGGTGAGATGACATTCTTGACCGGCTGACAACCAA
AGTAGACAAGTTAGATGTCAACATAAAAAGCACAGAAAGAAAAGTTCGACAACTC

Alignment

ORF - retro_nleu_2645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAYTKSYNPFDDDGEDEGARPAPWRDARDLPDGPDAPADRQQYLRQEVLRRAEATAASTSRSLALMYES
          M.AY.KSYNPF.DDGEDEGARPAPWRDARDLPDGPDAPADRQQYL.QEVLRRAEATAASTSRSLALMYES
Retrocopy MPAYPKSYNPFEDDGEDEGARPAPWRDARDLPDGPDAPADRQQYLQQEVLRRAEATAASTSRSLALMYES

Parental  EKVGVASSEELARQRGVLERTEKMVDKMDQDLKTSQKHINSIKSVFGGLVNYFKSKPVETPPEQNGTLAS
          EKVGVASSEELARQRGVLERTEKMVDKMDQD.KTSQKHINSIKSVFGGLVN.FKSKPVETPPEQNGTLAS
Retrocopy EKVGVASSEELARQRGVLERTEKMVDKMDQDSKTSQKHINSIKSVFGGLVNCFKSKPVETPPEQNGTLAS

Parental  QPNSRLKEAISTSKEQEAKYQASHPNLRKLDDTDPVPRGAGSAMSTDAYPKN-PHLRAYHQKIDSNLDEL
          QPNSRLKEAISTSKEQEAKYQASHPNLRKLDDTDPVPRGAGSAM.TDAYPK...HLRAYHQKI.SNLDEL
Retrocopy QPNSRLKEAISTSKEQEAKYQASHPNLRKLDDTDPVPRGAGSAMTTDAYPKS>YHLRAYHQKINSNLDEL

Parental  SMGLGRLKDIALGMQTEIEEQDDILDRLTTKVDKLDVNIKSTERKVRQL
          SMGLG.LKDIALGMQTEIE..DDILDRLTTKVDKLDVNIKSTERKVRQL
Retrocopy SMGLGCLKDIALGMQTEIEG*DDILDRLTTKVDKLDVNIKSTERKVRQL

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_2645 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015201	1 retrocopy	retro_cfam_1542,
Cavia porcellus	ENSCPOG00000003137	1 retrocopy	retro_cpor_1442,
Dasypus novemcinctus	ENSDNOG00000005913	4 retrocopies	retro_dnov_1401, retro_dnov_1855, retro_dnov_2001, retro_dnov_2364,
Nomascus leucogenys	ENSNLEG00000000108	1 retrocopy	retro_nleu_2645 ,
Otolemur garnettii	ENSOGAG00000013003	1 retrocopy	retro_ogar_3493,