RetrogeneDB ID: retro_nleu_1348

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397290.1:15995038..15995581(+)
• Located in intron of: ENSNLEG00000011899

Retrocopy information

• Ensembl ID: ENSNLEG00000018903
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARF3
• Ensembl ID: ENSNLEG00000017859
• Aliases: None
• Description: None

Sequence

>retro_nleu_1348
ATGGGCAATATCTTTGGAAACCTTCTCAAGAGCCTGATTGGGAAGAAGGAGATGCGCATCCTGATGGTGGGCCTGGATGC
CGCAAGAAAGACCACCATCCTATACAAGCTGAAACTGGGGGAGATCGTCACCACCATCCCTGCCATTGGGTTCAATGTGG
AGACAGTGGAGTATAAGAACATCAGCTTCACAGTGTGGGATGTGGGTGGCCAGGACAAGATTCGACCCCTGTGGGGACAC
TACTTCCAGAACACCCAAGGGTTGATATTTGTGGTCGACAGCAATGAGCGGGAGCGAGTAAATGAGGCCCGGGAAGAGCT
GATGAGAATGCTGGCGGAGGACGAGCTCCGGGATGCTGCACTCCTTGTCTTTGCAAACAAACAGGATCTGCCTAATGCTA
TGAACGCTGCTGAGATCACAGACAAGCTGGGCCTGCATTCCCTTCGTCACCGTAACTGGTACATTCAGGCCACCTGTGCC
ACCAGCGGGGACGGGCTGTACGAAGGCCTGGACTGGCTGGCCAATCAGCTCAAAAACAAGAAG

Alignment

ORF - retro_nleu_1348 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNIFGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGG
          MGNIFGNLLKSLIGKKEMRILMVGLDAA.KTTILYKLKLGEIVTTIP.IGFNVETVEYKNISFTVWDVGG
Retrocopy MGNIFGNLLKSLIGKKEMRILMVGLDAARKTTILYKLKLGEIVTTIPAIGFNVETVEYKNISFTVWDVGG

Parental  QDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEIT
          QDKIRPLW.HYFQNTQGLIFVVDSN.RERVNEAREELMRMLAEDELRDA.LLVFANKQDLPNAMNAAEIT
Retrocopy QDKIRPLWGHYFQNTQGLIFVVDSNERERVNEAREELMRMLAEDELRDAALLVFANKQDLPNAMNAAEIT

Parental  DKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLANQLKNKK
          DKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLANQLKNKK
Retrocopy DKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLANQLKNKK

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_1348 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 19 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008240	1 retrocopy	retro_acar_12,
Cavia porcellus	ENSCPOG00000025074	1 retrocopy	retro_cpor_92,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Homo sapiens	ENSG00000134287	1 retrocopy	retro_hsap_36,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Loxodonta africana	ENSLAFG00000004207	1 retrocopy	retro_lafr_115,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus	ENSMICG00000017545	1 retrocopy	retro_mmur_37,
Monodelphis domestica	ENSMODG00000013804	1 retrocopy	retro_mdom_241,
Mus musculus	ENSMUSG00000051853	1 retrocopy	retro_mmus_147,
Nomascus leucogenys	ENSNLEG00000007270	3 retrocopies	retro_nleu_2106, retro_nleu_2703, retro_nleu_2704,
Nomascus leucogenys	ENSNLEG00000014137	3 retrocopies	retro_nleu_210, retro_nleu_227, retro_nleu_2929,
Nomascus leucogenys	ENSNLEG00000017859	2 retrocopies	retro_nleu_1348 , retro_nleu_94,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Sarcophilus harrisii	ENSSHAG00000003635	2 retrocopies	retro_shar_25, retro_shar_364,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000004698	1 retrocopy	retro_ttru_1081,