RetrogeneDB ID: retro_ptro_3193

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:37467335..37468086(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LANCL3
• Ensembl ID: ENSPTRG00000021790
• Aliases: None
• Description: LanC lantibiotic synthetase component C-like 3 (bacterial) [Source:HGNC Symbol;Acc:24767]

Sequence

>retro_ptro_3193
ATGGACACCAAGCGCTGTTTCCCTTATCGCCTCGATGACTACCAGGGCAGCCTGCTGGCGGGCCATTGCGAGGAGGCGGT
GGCGTCCTTGGTCACCGCCACCATCCAGCGCATCCTCCAGGAGCTTCCCCCACTCGGGGCGGCGCCGAGGCCTGAGGGGC
GACGGCCAGGGCTAGCGGCTGCCAGGGGGGGTTTATGGCGGCGTGGCCGGAGTGGCGTATATGCTCTACCACGTCTCGCA
AAGCCCGCTTTTCGCCACGGCCCGGGAACGCTACCTGCGCTCAGCTGTGCGCCTCATGGACGCGTGCGCCCGCGCTGAGG
AGTGGGGCGAACCGGACGCCGACACCCGCGCTGCCTTCCTGCTCGGGGGCGCGGGCGTGTACGCCGTGGCCACGCTCGTA
TACCACGCCCTGGGCCGGTCCGACTACGTGCAGCCGCTGGGCAAGTTCCGGGCTCTGTGTGCCGTCTGCGCGCCGGTCTC
CTTCCTGGAGTGCGGCTCCGACGAGCTGTCTGTGGGCCGCGCGGGCTACCTGTGTGCCGCGCTGGCGCTCAAACAGAAAC
TCACCCAGGAGGTAAGAGGTAGCCCCGGCCGCGAGAGGGCGCTCGCCGCCTGCCCGGCCTCCCTTCCGGACTCCGTGGCT
CGGGCAGCACTGTCCGCTTGCTCTCCATGTTTTTGTTACTCTTGTTGTGGTGCTAGCATTTCTTCAGTCTCTTGAGGTCT
GTCTCCTGCTTTTGTCCGTCTTCTTTCCTTT

Alignment

ORF - retro_ptro_3193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.38 %
• Parental protein coverage: 59.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDTKRCFANRFDDYQGSLLAGQCEEAVAPLVTATIERILQELPPLG-GGAEARGATAGASACQGG-LYGG
          MDTKRCF..R.DDYQGSLLAG.CEEAVA.LVTATI.RILQELPPLG.GGAEA.GATA.AS.CQGG..YGG
Retrocopy MDTKRCFPYRLDDYQGSLLAGHCEEAVASLVTATIQRILQELPPLG<GGAEA*GATARASGCQGG<VYGG

Parental  VAGVAYMLYHVSQSPLFATARERYLRSAKRLIDACARAEEWGEPDADTRAAFLLGGAGVYAVATLVYHAL
          VAGVAYMLYHVSQSPLFATARERYLRSA.RL.DACARAEEWGEPDADTRAAFLLGGAGVYAVATLVYHAL
Retrocopy VAGVAYMLYHVSQSPLFATARERYLRSAVRLMDACARAEEWGEPDADTRAAFLLGGAGVYAVATLVYHAL

Parental  GRSDYVQPLGKFRALCAVCAPVSFLECGSDELFVGRAGYLCAALVLKQKLAQEVL-TPAQIKSI--CQAI
          GRSDYVQPLGKFRALCAVCAPVSFLECGSDEL.VGRAGYLCAAL.LKQKL.QEV...P........C.A.
Retrocopy GRSDYVQPLGKFRALCAVCAPVSFLECGSDELSVGRAGYLCAALALKQKLTQEVRGSPGRERALAACPAS

Parental  L-DSGKQYAIKKRKPFPLMYSYYGTEYLGAAHGLSSILQMLLSY
          L.DS....A.....P....YS..G........GLS.....LLS.
Retrocopy LPDSVARAALSACSPC-FCYSCCGASISSVS*GLSPAFVRLLSF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.02 RPM	0.38 RPM
SRP007412_cerebellum	0.00 RPM	0.29 RPM
SRP007412_heart	0.00 RPM	1.43 RPM
SRP007412_kidney	0.00 RPM	0.89 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.21 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3193 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3193 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000014625	1 retrocopy	retro_meug_1916,
Nomascus leucogenys	ENSNLEG00000000916	1 retrocopy	retro_nleu_2178,
Pan troglodytes	ENSPTRG00000021790	1 retrocopy	retro_ptro_3193 ,