RetrogeneDB ID: retro_pabe_211

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:98762638..98763583(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000017868
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CALU
• Ensembl ID: ENSPPYG00000017982
• Aliases: None
• Description: Calumenin [Source:UniProtKB/Swiss-Prot;Acc:Q5RDD8]

Sequence

>retro_pabe_211
ATGGACCTGCAACAGTTTCTTATGTGCCTGTCCCTGTGCACAGCCTTTGCCTTGAGCAAGCCCACAGAAAAGAAGGACCG
TGTACATCATGAGCCTCAGCTCAGTGACAAGGTTCATAATGATGCTCAGAGTTTTGATTATGACCATGATGCCTTCCTGG
GTGCTGAAGAAGCAAAGACCTTTGATCAGCTGACACCAGAAGAGAGCAAGGAAAGGCTTGGAAAGACTGTAAGTAAAATA
GATGACAACAAGGACGGGTTTGTCACTGTGGATGAGCTCAAAGACTGGATTAAATTTGCACAAAAGTGCTGGATTTACGA
GGATGTAGAGCGACAGTGGAAGGGGCATGACCTCAATGAGGACGGCCTCGTTTCCTGGGAGGAGTATAAAAATGTCACCT
ACGGCTGCGTTTTAGATGATCCAGACCCTGATGATGGATTTAACTATAAACAGATGATGGTTAGAGATGAGCAGAGGTTT
AAAATGGCAGACAAGGATGGAGACCTCATTGCCACAAAGGAGGAGTTCACAGCTTTCCTGCACCCTGAGGAGTATGACTA
CATGAAAGATATAGTATTGCAGGAAATAATGGAAGATATAGATAAGAATGCTAATGGTTTCATTGATCTAGAAGAGTATA
TTGGTGACATGTACAGCCATGATGGGAATACTGATGAGCCAGAATGGGTAAAGACAGAGCGAGAGCAGTTTGTTGAGTTT
CGGGATAAGAACTGTGATGGGAAGATGGACAAGGAAGAGACCAAAGACTGGATCCTTCCCTCAGACTATGATCATGCAGA
GGCAGAAGCCAGGCACCTGGTCTATGAATCAGACCAAAACAAGGATGGCAAGCTTACCAAGGAGGAGATTGTTGACAAGT
ATGACTTATTTGTTGGCAGCCAGGCCACAGATTTTGGGGAGGCCTTAGTACGGCATGATGAGTTT

Alignment

ORF - retro_pabe_211 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDLRQFLMCLSLCTAFALSKPTEKKDRVHHEPQLSDKVHNDAQSFDYDHDAFLGAEEAKTFDQLTPEESK
          MDL.QFLMCLSLCTAFALSKPTEKKDRVHHEPQLSDKVHNDAQSFDYDHDAFLGAEEAKTFDQLTPEESK
Retrocopy MDLQQFLMCLSLCTAFALSKPTEKKDRVHHEPQLSDKVHNDAQSFDYDHDAFLGAEEAKTFDQLTPEESK

Parental  ERLGKIVSKIDDDKDGFVTVDELKDWIKFAQKRWIYEDVERQWKGHDLNEDGLVSWEEYKNATYGYVLDD
          ERLGK.VSKIDD.KDGFVTVDELKDWIKFAQK.WIYEDVERQWKGHDLNEDGLVSWEEYKN.TYG.VLDD
Retrocopy ERLGKTVSKIDDNKDGFVTVDELKDWIKFAQKCWIYEDVERQWKGHDLNEDGLVSWEEYKNVTYGCVLDD

Parental  PDPDDGFNYKQMMVRDERRFKMADKDGDLIATKEEFTAFLHPEEYDYMKDIVVQETMEDIDKNADGFIDL
          PDPDDGFNYKQMMVRDE.RFKMADKDGDLIATKEEFTAFLHPEEYDYMKDIV.QE.MEDIDKNA.GFIDL
Retrocopy PDPDDGFNYKQMMVRDEQRFKMADKDGDLIATKEEFTAFLHPEEYDYMKDIVLQEIMEDIDKNANGFIDL

Parental  EEYIGDMYSHDGNTDEPEWVKTEREQFVEFRDKNRDGKMDKEETKDWILPSDYDHAEAEARHLVYESDQN
          EEYIGDMYSHDGNTDEPEWVKTEREQFVEFRDKN.DGKMDKEETKDWILPSDYDHAEAEARHLVYESDQN
Retrocopy EEYIGDMYSHDGNTDEPEWVKTEREQFVEFRDKNCDGKMDKEETKDWILPSDYDHAEAEARHLVYESDQN

Parental  KDGKLTKEEIVDKYDLFVGSQATDFGEALVRHDEF
          KDGKLTKEEIVDKYDLFVGSQATDFGEALVRHDEF
Retrocopy KDGKLTKEEIVDKYDLFVGSQATDFGEALVRHDEF

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	0.06 RPM	60.76 RPM
SRP007412_cerebellum	0.00 RPM	38.06 RPM
SRP007412_heart	0.18 RPM	146.06 RPM
SRP007412_kidney	0.07 RPM	39.15 RPM
SRP007412_liver	0.03 RPM	59.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_211 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_211 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010477	1 retrocopy	retro_dnov_863,
Pongo abelii	ENSPPYG00000003385	1 retrocopy	retro_pabe_2976,
Pongo abelii	ENSPPYG00000017982	1 retrocopy	retro_pabe_211 ,
Pan troglodytes	ENSPTRG00000019668	1 retrocopy	retro_ptro_6,