RetrogeneDB ID: retro_pabe_136

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:127768568..127769024(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000025839
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000009938
• Aliases: None
• Description: None

Sequence

>retro_pabe_136
CTTTTGGACAGAGTCTTCAAAGCCAGTTATACCTTCCAAGAGGTCCATGTTTTCATCCAGGGCTTGCCAGAAGGCCTGGA
AGTGGCAGGTCTCCAGCAGGTCCCCAAGGTACAAAATCTGTCAGATTGGCCGTTCTTCTTGATGTGCCTGGTCGATCATG
CACTTGCACAGGGTGAAGTCTGTGTGCGGCAGGTTGGTGAGGGCCTTCAGCAGGATCTGGGCAGTGACCGTGGTCTGAAA
GAAGGCTGGGTTGAACTGGTACAGCTTCAGGACAGCCAGGTTGGCTTCCAGATCATAGGCGTTTTCCTTGGCCTGCATCT
CTACATAGCGCTCCAGGGTGGCCAGGTTGTCAGGGTTGTACCTGTCGATACCCTTGAGCAACTTGCCCATGTTGGCTCTC
ATCTGCTCAAACATCGCCATGACTTCTGTCACCTTCCACAACCAGGGCTGGAGGCT

Alignment

ORF - retro_pabe_136 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.46 %
• Parental protein coverage: 98.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSDRVFKASYTFQEVHVFIQGLPEGLEVAGLQQVPKVQNLSDWPFFLLMCLVDHALAQGEVCVRQVGEGL
          L.DRVFKASYTFQEVHVFIQGLPEGLEVAGLQQVPKVQNLSDWPFF.LMCLVDHALAQGEVCVRQVGEGL
Retrocopy LLDRVFKASYTFQEVHVFIQGLPEGLEVAGLQQVPKVQNLSDWPFF-LMCLVDHALAQGEVCVRQVGEGL

Parental  QQDLGGDRGLKEGWVELLQLQDSQVGFQIIGIFLGLRLYIALQGGQVLRIVPVDTLEQLAHVGSHLLKHR
          QQDLG.DRGLKEGWVEL.QLQDSQVGFQIIG.FLGL.LYIALQGGQV.R.VPVDTLEQLAHVGSHLLKHR
Retrocopy QQDLGSDRGLKEGWVELVQLQDSQVGFQIIGVFLGLHLYIALQGGQVVRVVPVDTLEQLAHVGSHLLKHR

Parental  HDFCRLPKPGLEA
          HDFC.LP.PGLEA
Retrocopy HDFCHLPQPGLEA

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	0.28 RPM	0.00 RPM
SRP007412_cerebellum	0.49 RPM	0.00 RPM
SRP007412_heart	0.12 RPM	0.00 RPM
SRP007412_kidney	0.13 RPM	0.00 RPM
SRP007412_liver	0.03 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_136 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_136 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000021632	2 retrocopies	retro_mmul_1542, retro_mmul_2098,
Pongo abelii	ENSPPYG00000009938	2 retrocopies	retro_pabe_136 , retro_pabe_2466,