RetrogeneDB ID: retro_nleu_1229

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397285.1:10776757..10777270(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018588
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CIAPIN1
• Ensembl ID: ENSNLEG00000002876
• Aliases: None
• Description: None

Sequence

>retro_nleu_1229
TCTGTTCGAGAACACCTTGGTCATGAAAGTGACAGCCTGCTGTTTGTTCAGATCACAGGCAAAAAAACAAACTTTGAAGT
GGTTTCTTCTAGTCAGCTTAAGTTTTCCATCACCATGAAGTCTTCTCCTTCAGGGAAGCCTGCTGTGGACCCTGCTGCTG
CCAAGCTGTGGACCCTCTCAGCCAACGATATGGAGGACGACAGCATGGACCTCATTGACTCAGATGAGCTGCTAGATCCA
GAAGATTTGAAGAAGCCAGATCCGGCTTCCCTGCAGGCTACTTCTTGTGGGGAAGGGAAAAAGAGGAAGGCCTGTAAGAA
CTGCACCTGTGGCCTTGCCGAAGAACTGGAAAAAGAGAAGTCAAGGGAACAGATGAGCTCCCAACCCAAGTCAGCTTGTG
GAAACTGCTACCTGGGCGATGCCTTCCACTGTGCCAGCTGCCCCTACCTTGGGATGCCAGCCTTCAAACCTGAGGAAAAG
GTGCTTCTGAGCAATAGCAATCTTCACGATGCC

Alignment

ORF - retro_nleu_1229 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.98 %
• Parental protein coverage: 54.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVREHLGHESDNLLFVQITGKKPNFEVGSSRQLKLSITKKSSPSVKPAVDPAAAKLWTLSANDMEDDSMD
          SVREHLGHESD.LLFVQITGKK.NFEV.SS.QLK.SIT.KSSPS.KPAVDPAAAKLWTLSANDMEDDSMD
Retrocopy SVREHLGHESDSLLFVQITGKKTNFEVVSSSQLKFSITMKSSPSGKPAVDPAAAKLWTLSANDMEDDSMD

Parental  LIDSDELLDPEDLKKPDPASLRAASCGEGKKRKACKNCTCGLAEELEKEKSREQMSSQPKSACGNCYLGD
          LIDSDELLDPEDLKKPDPASL.A.SCGEGKKRKACKNCTCGLAEELEKEKSREQMSSQPKSACGNCYLGD
Retrocopy LIDSDELLDPEDLKKPDPASLQATSCGEGKKRKACKNCTCGLAEELEKEKSREQMSSQPKSACGNCYLGD

Parental  AFRCASCPYLGMPAFKPGEKVLLSDSNLHDA
          AF.CASCPYLGMPAFKP.EKVLLS.SNLHDA
Retrocopy AFHCASCPYLGMPAFKPEEKVLLSNSNLHDA

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_1229 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012055	1 retrocopy	retro_cjac_2575,
Homo sapiens	ENSG00000005194	1 retrocopy	retro_hsap_1875,
Gorilla gorilla	ENSGGOG00000012402	1 retrocopy	retro_ggor_1372,
Macaca mulatta	ENSMMUG00000020472	1 retrocopy	retro_mmul_1719,
Monodelphis domestica	ENSMODG00000013522	1 retrocopy	retro_mdom_456,
Nomascus leucogenys	ENSNLEG00000002876	1 retrocopy	retro_nleu_1229 ,
Pongo abelii	ENSPPYG00000007388	2 retrocopies	retro_pabe_1260, retro_pabe_1556,
Pan troglodytes	ENSPTRG00000008155	1 retrocopy	retro_ptro_1258,