RetrogeneDB ID: retro_pabe_3394

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:28631528..28631956(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAGE3
• Ensembl ID: ENSPPYG00000020881
• Aliases: None
• Description: L antigen family, member 3 [Source:HGNC Symbol;Acc:26058]

Sequence

>retro_pabe_3394
ATGCGGGACGTGGATGCAGACGCAGGCGGAGGCGCCAACTGCGGGGATGGCCAGGGTGATCACAGCTGCCCCGGGGGCGC
GGACACCCCGGCAGCTCCGGCCAGCAGAGCTCCCCTACCGCACGCGTCAGGTCCTGGCAGAGACGCGGCGTCTGTGGCCA
GGGGCCAGGAATGCGGCCGCACATATTCACCCTCAGCGTGCCTTTCCCGACCCCCTTAGAGGCAGAAATTGCCCATGGGT
CCCTGGCTCCAGATGCCGAGCCTCACCAAAGGGTGGTTGGGAAGGATCTCACAGTGAGCGGCAGGATCCTGGCCGTCCGC
TGGAAAGCTGAAGACTGTCGCCTGCTCCGAATTTCCGTTATCAACTTTCTCGACCATCTTTCTCTGGTGGTGCGGACCCT
GCAGCACTTTGGGCCCCCAGTTTCCCGC

Alignment

ORF - retro_pabe_3394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREADAHAGGGADGGDGQGGHSCRGVVDTAAAPAGGAPPAHAPGSSRDAASAARGS-GMRPHIFTLSVPF
          MR..DA.AGGGA..GDGQG.HSC.G..DT.AAPA..AP..HA.G..RDAAS.ARG..GMRPHIFTLSVPF
Retrocopy MRDVDADAGGGANCGDGQGDHSCPGGADTPAAPASRAPLPHASGPGRDAASVARGQ<GMRPHIFTLSVPF

Parental  PTPLEAEIAHGSLAPDAEPHQRVIGKDLTVSGRILVVRWKAEDCRLLRISVINFLDQLSLVVRTMQRFGP
          PTPLEAEIAHGSLAPDAEPHQRV.GKDLTVSGRIL.VRWKAEDCRLLRISVINFLD.LSLVVRT.Q.FGP
Retrocopy PTPLEAEIAHGSLAPDAEPHQRVVGKDLTVSGRILAVRWKAEDCRLLRISVINFLDHLSLVVRTLQHFGP

Parental  PVSR
          PVSR
Retrocopy PVSR

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	2.10 RPM	18.14 RPM
SRP007412_cerebellum	1.82 RPM	10.94 RPM
SRP007412_heart	1.17 RPM	1.81 RPM
SRP007412_kidney	3.85 RPM	10.74 RPM
SRP007412_liver	2.82 RPM	7.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3394 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3394 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4244

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024143	1 retrocopy	retro_dnov_244,
Dipodomys ordii	ENSDORG00000009093	1 retrocopy	retro_dord_448,
Homo sapiens	ENSG00000196976	1 retrocopy	retro_hsap_4244,
Gorilla gorilla	ENSGGOG00000013507	1 retrocopy	retro_ggor_2845,
Macaca mulatta	ENSMMUG00000007739	1 retrocopy	retro_mmul_1145,
Mus musculus	ENSMUSG00000015289	2 retrocopies	retro_mmus_1411, retro_mmus_1665,
Nomascus leucogenys	ENSNLEG00000014285	1 retrocopy	retro_nleu_1373,
Ochotona princeps	ENSOPRG00000003778	2 retrocopies	retro_opri_196, retro_opri_549,
Pongo abelii	ENSPPYG00000020881	1 retrocopy	retro_pabe_3394 ,
Rattus norvegicus	ENSRNOG00000037249	1 retrocopy	retro_rnor_595,
Sus scrofa	ENSSSCG00000025528	1 retrocopy	retro_sscr_94,