RetrogeneDB ID: retro_pabe_1349

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:35473283..35474087(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOCS1
• Ensembl ID: ENSPPYG00000016580
• Aliases: None
• Description: molybdenum cofactor biosynthesis protein 1 [Source:RefSeq peptide;Acc:NP_001126377]

Sequence

>retro_pabe_1349
GCGCGGCCACTGTCCCGGATGCTGCGGCGGCTCCTAAGATCCAACGCCACGGAGCTGCAGCTCAGGGGTTCGGGTGATGC
CGCTCTGCCCCGGCGAGTCCCCGCAAGCTGCCTCAGAGGAGCTGTCCAGGCGGAGGCAGTTCTTGCGGGAGCAGGAGGCC
CCCTTCTCCGCCTTCCTCACAGACAGCTTCGGCCGGCAGCACAGCTACCTGCGGATCTCCCTCCCGGAGAAGTGCAACCT
CAGATGTCAGTACTGCATGCCGGAGGAAGGGGTCCCGCTGACCCCCAAGGCCAACCTGCTGACCACAAAAGAGATTCTGA
CCCTCGCCTGGCTCTTTGTGAAGGAAGGCATCGAAAAGATCCAGCTCACGGGCGGAGAGCCGCTCATCCAGCCGTACGTG
GTGGACATTGTGGCCCAGCTCCACCGACTGGAAGGGCTGAGGACCATCGGTGTCACCACCAATGGCATCAACCTGGCCCG
GCTGCTGCCCCAGCTTCAGAAGGCTGGTCTCAGCGCCATCAACATCAGCCTGGACACACTGGTGCCTGCCAAGTTTGAGT
TCATTGTCCGCAGGAAAGTCTTCCACAAGGTCATGGAGGGCATCCACAAGGCCATCGAGCCAGGCTACAACCCTGTGAAG
GTGAACTGTGTGGTGATGCGAGGCCTTAACGAGGATGAACTCCTGGACTTTGCGGCCTTGACCAAGGGCCTCCCCCTGGA
TGTGCGCTTCATAGAGTACATGCCCTTTGATGGCAACAAGTGGAACTTCAGGAAGATGGTCGCTATAAGGAGATGCTAGA
AACT

Alignment

ORF - retro_pabe_1349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 69.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARPLSRMLWRLLRSSA-RSCSSGAPVTQPCPGESARAASEELSRRRQFLREHAAPFSAFLTDSFGRQHSY
          ARPLSRML.RLLRS.A.RSCSSG..V...CPGES..AASEELSRRRQFLRE..APFSAFLTDSFGRQHSY
Retrocopy ARPLSRMLRRLLRSNA>RSCSSGVRVMPLCPGESPQAASEELSRRRQFLREQEAPFSAFLTDSFGRQHSY

Parental  LRISLTEKCNLRCQYCMPEEGVPLTPKANLLTTEEILTLARLFVKEGVDKIRLTGGEPLIRPDVVDIVAQ
          LRISL.EKCNLRCQYCMPEEGVPLTPKANLLTT.EILTLA.LFVKEG..KI.LTGGEPLI.P.VVDIVAQ
Retrocopy LRISLPEKCNLRCQYCMPEEGVPLTPKANLLTTKEILTLAWLFVKEGIEKIQLTGGEPLIQPYVVDIVAQ

Parental  LQRLEGLRTIGVTTNGINLARLLPQLQKAGLSAINISLDTLVPAKFEFIVRRKGFHKVMEGIHKAIELGY
          L.RLEGLRTIGVTTNGINLARLLPQLQKAGLSAINISLDTLVPAKFEFIVRRK.FHKVMEGIHKAIE.GY
Retrocopy LHRLEGLRTIGVTTNGINLARLLPQLQKAGLSAINISLDTLVPAKFEFIVRRKVFHKVMEGIHKAIEPGY

Parental  NPVKVNCVVMRGLNEDELLDFAALTEGLPLDVRFIEYMPFDGNKWNFKKMVS-YKEMLDT
          NPVKVNCVVMRGLNEDELLDFAALT.GLPLDVRFIEYMPFDGNKWNF.KMV..YKEML.T
Retrocopy NPVKVNCVVMRGLNEDELLDFAALTKGLPLDVRFIEYMPFDGNKWNFRKMVA<YKEMLET

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	13.44 RPM
SRP007412_cerebellum	0.00 RPM	14.23 RPM
SRP007412_heart	0.00 RPM	6.95 RPM
SRP007412_kidney	0.03 RPM	98.28 RPM
SRP007412_liver	0.00 RPM	37.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1349 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1349 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1349 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
Gorilla gorilla	ENSGGOG00000008943	1 retrocopy	retro_ggor_1234,
Pongo abelii	ENSPPYG00000016580	1 retrocopy	retro_pabe_1349 ,