RetrogeneDB ID: retro_pabe_104

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:32797319..32798402(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000009053
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000014154
• Aliases: None
• Description: None

Sequence

>retro_pabe_104
ATGGCGCCCCTCAGAACAAGTGTATTGCTGTGGAGCCTCTTGAGGAGTTCTCCGGGCGTGGAACGGGTCTGTTTGCGGGC
TCGAATCCAGCCCTGGCACGGTGGCCTGCTCCAACCGCAACCTTGCTCTTTCGAGATGGGGCTGCCACGCCGCCGGTTCA
GCTCCGACGCCGCAGAATCTGGTAGCCCAGAGACCAAGAAACCTACATTTATGGATGAGGAAGTTCAAAGCATACTCACA
AAAATGACAGGCTTGAACTTGCAGAAGACTTTTAAGCCAGCTATACAAGAACTGAAGCCACCAACCTATAAGCTAATGAC
TCAGGCACAGTTGGAAGAGGCTACAAGACAGGCAGTTGAGGCAGCTAAAGTACGATTAAAAATGCCACCAGTTCTGGAAG
AGCGAGTACCAATAAATGATGTGTTAGCTGAAGATAAGATTTTGGAAGGAACAGAAACAACCAAATATGTGTTTACTGAT
ATATCATATAGCATACCACACCGGGAGCGTTTTATTGTCGTCAGAGAACCAAGTGGCACACTACGCAAAGCCTTTTGGGA
AGAACGGGACCGAATGATACAAGTTTATTTCCCAAAAGAAGGTCGTAAAATTTTGACACCAATAATTTTCCAGGAAGAGA
ATCTTAGGACTATGTATAGCCAGGACAGGCATGTTGATGTCCTCAATCTCTGCTTTGCCCAGTTTGAGCCAGATTCCACT
GAGTATATCAAGGTTCATCACAAGACCTATGAAGATATAGATAAACATGGAAAATATGACCTTTTACGTTCAACGAGATA
CTTTGGTGGAATGGTGTGGTATTTTGTAAATAATAAAAAGATTGATGGTTTGCTGATTGACCAGATTCAGAGAGATTTAA
TCGATGATGCAACCAACTTGGTCCAGCTGTATCACATGCTCCATCCAGACGGCCAGTCGGCTCAAGAGGCCAAGGATCAG
GCTGCTGAGGGAATAAATTTAATCAAGGTCTTTGCAAAAACAGAAGCACAGAAGGGAGCCTATATAGAACTAACACTGCA
AACTTATCAAGAAGCACTCAGTCGCCATTCTGCAGCTTCCTAA

Alignment

ORF - retro_pabe_104 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.44 %
• Parental protein coverage: 98.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTSVLLWSLLRSSPGVERVCLRARIQPWRGGLLQPQPCSFEMGLPRRRFSSDAAESGSPETKKPTFMDEE
          RTSVLLWSLLRSSPGVERVCLRARIQPW.GGLLQPQPCSFEMGLPRRRFSSDAAESGSPETKKPTFMDEE
Retrocopy RTSVLLWSLLRSSPGVERVCLRARIQPWHGGLLQPQPCSFEMGLPRRRFSSDAAESGSPETKKPTFMDEE

Parental  VQSILTKMTGLNLQKTFKPAIQELKPPTYKLMTQAQLEEATRQAVEAAKVRLKMPPVLEERVPINDVLAE
          VQSILTKMTGLNLQKTFKPAIQELKPPTYKLMTQAQLEEATRQAVEAAKVRLKMPPVLEERVPINDVLAE
Retrocopy VQSILTKMTGLNLQKTFKPAIQELKPPTYKLMTQAQLEEATRQAVEAAKVRLKMPPVLEERVPINDVLAE

Parental  DKILEGTETTKYVFTDISYSIPHRERFIVVREPSGTLRKAFWEERDRMIQVYFPKEGRKILTPIISQEEN
          DKILEGTETTKYVFTDISYSIPHRERFIVVREPSGTLRKAFWEERDRMIQVYFPKEGRKILTPII.QEEN
Retrocopy DKILEGTETTKYVFTDISYSIPHRERFIVVREPSGTLRKAFWEERDRMIQVYFPKEGRKILTPIIFQEEN

Parental  LRTMYSQDRHVDVLNLCFAQFEPDSTEYIKVHHKTYEDIDKHGKYDLLRSTRYFGGMVWYFVNNKKIDGL
          LRTMYSQDRHVDVLNLCFAQFEPDSTEYIKVHHKTYEDIDKHGKYDLLRSTRYFGGMVWYFVNNKKIDGL
Retrocopy LRTMYSQDRHVDVLNLCFAQFEPDSTEYIKVHHKTYEDIDKHGKYDLLRSTRYFGGMVWYFVNNKKIDGL

Parental  LIDQIQRDLIDDATNLVQLYHMLHPDGQSAQEAKDQAAEGINLIKVFAKTEAQKGAYIELTLQTYQEALS
          LIDQIQRDLIDDATNLVQLYHMLHPDGQSAQEAKDQAAEGINLIKVFAKTEAQKGAYIELTLQTYQEALS
Retrocopy LIDQIQRDLIDDATNLVQLYHMLHPDGQSAQEAKDQAAEGINLIKVFAKTEAQKGAYIELTLQTYQEALS

Parental  RHSAAS
          RHSAAS
Retrocopy RHSAAS

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	6.86 RPM	7.46 RPM
SRP007412_cerebellum	5.72 RPM	13.01 RPM
SRP007412_heart	12.52 RPM	4.21 RPM
SRP007412_kidney	11.40 RPM	5.54 RPM
SRP007412_liver	8.66 RPM	4.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_104 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007610	1 retrocopy	retro_cfam_123,
Pongo abelii	ENSPPYG00000014154	1 retrocopy	retro_pabe_104 ,