RetrogeneDB ID: retro_pabe_1198

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:82720993..82721328(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000005032
• Aliases: None
• Description: None

Sequence

>retro_pabe_1198
ATGCTTTTAACCAGATTTGAACAGAAGAATGGCCACTTGGCCCAAGTAGAAGTAGATGAAGTGTTTGGTTTCATGTGTCA
CGTAACTACTGAAGTTCCTCCCCACGATGCAATGTCAGGTGGGATTGTACTTCTTGTCACATTCCTTCTTGATATGAGCC
ACAGCGTTCCTCTCTTTGTTGTATTTCTCCAGCGCCTGAGTAGCGCACTCCACCGAGTTCTGTTGCATCTCTTCCGACAT
GTCCCGCATTTTTGATCACGGGCCTTTTGGGTCACACATGGTTACCCATGGAGAAGGGGGCTTGGCTGACTGCAACGGTC
TCCTGGGGAAGGTGC

Alignment

ORF - retro_pabe_1198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLLTRFEQKNGHLAQVEVDEVFGFMCHVTTEVPPHDAMPGGIVLLVKFLLLDMSRNVLLYVVFLQRLSSA
          MLLTRFEQKNGHLAQVEVDEVFGFMCHVTTEVPPHDAM.GGIVLLV.F.LLDMS..V.L.VVFLQRLSSA
Retrocopy MLLTRFEQKNGHLAQVEVDEVFGFMCHVTTEVPPHDAMSGGIVLLVTF-LLDMSHSVPLFVVFLQRLSSA

Parental  LHRVLLHLFRHV-RIFDHGLSVAHGY-RGEGG-WPTATVSWGRC
          LHRVLLHLFRHV.RIFDHG....H....GEGG.W.TATVSWGRC
Retrocopy LHRVLLHLFRHV>RIFDHGPFGSHMVTHGEGG>WLTATVSWGRC

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	0.00 RPM	4.70 RPM
SRP007412_cerebellum	0.00 RPM	1.70 RPM
SRP007412_heart	0.00 RPM	1.11 RPM
SRP007412_kidney	0.00 RPM	1.09 RPM
SRP007412_liver	0.00 RPM	1.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1198 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1198 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1113
Macaca mulatta	retro_mmul_2269

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000009268	3 retrocopies	retro_etel_1297, retro_etel_390, retro_etel_781,
Gorilla gorilla	ENSGGOG00000008793	4 retrocopies	retro_ggor_1066, retro_ggor_1113, retro_ggor_2055, retro_ggor_3078,
Macaca mulatta	ENSMMUG00000001195	6 retrocopies	retro_mmul_1463, retro_mmul_1723, retro_mmul_1897, retro_mmul_2269, retro_mmul_470, retro_mmul_835,
Pongo abelii	ENSPPYG00000005032	6 retrocopies	retro_pabe_1134, retro_pabe_1198 , retro_pabe_1215, retro_pabe_1469, retro_pabe_2371, retro_pabe_2459,
Tupaia belangeri	ENSTBEG00000008820	3 retrocopies	retro_tbel_1196, retro_tbel_1765, retro_tbel_695,