RetrogeneDB ID: retro_pabe_3306

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:18780003..18780555(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGCB
• Ensembl ID: ENSPPYG00000014780
• Aliases: None
• Description: beta-sarcoglycan [Source:RefSeq peptide;Acc:NP_001125865]

Sequence

>retro_pabe_3306
AAGTCCATGCGTGAGAAGGCTGTTGAGAGAAGGAATGTCAATAAAGAGCACAACAGTAACTTTAAAGCTGGATACATTCC
GATCGATGGAGATCGTCTCCACAAAACAGGGTTGAGAGGAAGAAAGGGCAATTTAGCCATCTGTGTGATTATCCTCTTGT
TTATCCTGGCTGTCACCAATTTAATAATAACACTTGTTATTTGGGCCGTGATTCGCATTGGACCAAATGGCTGTGATAGT
ATGGAGTTTCATGAAAGTGGCCTGCTTCAATTTAAGCAAGTATCTGACATGGGAGTGATCCATCCTCTTTATAAAAGCAC
AGTAGGAGGAAGGCGAAATGAAAATTTGGTCATCACTGGCAACAACCAGCCTATTGTTTTTCAGCAAGGGACAACAAAGC
TCAGTGTAGAAAACAACAAAACTTCTATTACAAGTGACATCGGCATGCAGTTTTTTGACCCGTGGACTCAAAATATCTTA
TTCAGCACAGACTATGAAACCCATGAGTTTCATTTGCCAAGTGGAGTGAAAAGTTTGAATGTTCAAAAAAGC

Alignment

ORF - retro_pabe_3306 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.28 %
• Parental protein coverage: 57.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSMREKAVERRNVNKEHNSNFKAGYIPIDEDRLHKTGLRGRKGNLAICVIILLFILAVINLIITLVIWAV
          KSMREKAVERRNVNKEHNSNFKAGYIPID.DRLHKTGLRGRKGNLAICVIILLFILAV.NLIITLVIWAV
Retrocopy KSMREKAVERRNVNKEHNSNFKAGYIPIDGDRLHKTGLRGRKGNLAICVIILLFILAVTNLIITLVIWAV

Parental  IRIGPNGCDSMEFHESGLLRFKQVSDMGVIHPLYKSTVGGRRNENLVITGNNQPIVFQQGTTKLSVENNK
          IRIGPNGCDSMEFHESGLL.FKQVSDMGVIHPLYKSTVGGRRNENLVITGNNQPIVFQQGTTKLSVENNK
Retrocopy IRIGPNGCDSMEFHESGLLQFKQVSDMGVIHPLYKSTVGGRRNENLVITGNNQPIVFQQGTTKLSVENNK

Parental  TSITSDIGMQFFDPRTQNILFSTDYETHEFHLPSGVKSLNVQKA
          TSITSDIGMQFFDP.TQNILFSTDYETHEFHLPSGVKSLNVQK.
Retrocopy TSITSDIGMQFFDPWTQNILFSTDYETHEFHLPSGVKSLNVQKS

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	15.43 RPM
SRP007412_cerebellum	0.00 RPM	22.86 RPM
SRP007412_heart	0.00 RPM	19.09 RPM
SRP007412_kidney	0.00 RPM	12.10 RPM
SRP007412_liver	0.00 RPM	8.91 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3306 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3306 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3306 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000014780	2 retrocopies	retro_pabe_3305, retro_pabe_3306 ,