RetrogeneDB ID: retro_pabe_3577

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:18307060..18309007(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RABL6
• Ensembl ID: ENSPPYG00000019786
• Aliases: None
• Description: RAB, member RAS oncogene family-like 6 [Source:HGNC Symbol;Acc:24703]

Sequence

>retro_pabe_3577
ATGTTTTCCGCCCTGAAGAAGCTGGTGGGGTCGGACCAGGCCCCGGGCCGGGACAAGAACATCCCCACCGGGCTGCAGTC
CATGAACCAGGCGTTGCAGAGGCGTTTCGCCAAGGGGGTGCAGTACAACATGAAGATAGTGATCCGGGGAGACAGGAACA
CGGGCAAAACAGCGCTGTGGCAGCGCCTGCAGGGCCGGCCGTTCGTGGAGGAGTACGTCCCCACGCAGGAGATCCAGGTC
ACCAGCATCCACTGCAGCTACAAGACCACGGATGACATCGTGAAGGTTGAAGTCTGGGATGTGGTAGACAAAGGAAAATG
CAAAAAGCGAGGCGACGGCTTAAAAATGGAGAACGACCCCCAGGAGGCGGAGTCCGAAATGGCCCTGGATGCTGAGTTCC
TGGACGTGTACAAGAACTGCAACGGGGTGGTCATGATGTTCGATATCACCAAGCAGTGGACCTTCAATTACATTCTCCAG
GAGCTTCCGAAAGTGCCCACCCATGTGCCAGTGTGCGTGCTGGGGAACTACCGGGACATGGGCGAGCACCGAGTCATCCT
GCCGGACGACGTGCGTGACTTCATCGACAACCTGGACAGACCTCCAGGTTCCTCCTACTTCCGCTACGCTGAGTCTTCCA
TGAAGAACAGCTTCGGCTTAAAGTACCTTCATAAGTTCTTCAATATCCCATTTTTGCAGCTTCAGAGGGAGACGCTGTTG
CGGCAGCTGGAGACAAACCAGCTGGACATGGACACCACACTGGAGGAGCTGTCAGTGCAGCAGGAGACGGAGGACCAGAA
CTACGGCATCTTCCTGGAGATGATGGAGGCTCGCAGCCGCGGCCATGCGTCCCCACTGGCGGCCAACGGGCAGAGCCCAT
CCTCGGGCTCCCAGTCAACAGTGGTGCCTCCAGGCGCTGTGTCCACGGGGAGCTCCAGCCCCGGCACACCCCAGCCCGCC
CCACAGCTGCCCCTCAATGCCGCCCCACCATCCTCTGTGCCCCCGTACCACCCTCAGAGGCCCTGCCCCCATCTGCGTGC
CCCTCAGCCCCCGCCCCACGGCGCAGCATCATCTCTAGGCTGTTTGGGACGTCACCTGCTGCCGAGGCAGCCCCTCCACC
TCCAGAGCCAGTCCCGGCCGCAGAGGCCCCAGCAAGTCCAGAGTGTGGAGGACTTTGTTCCCGATGACCGCCTGGACCGC
AGCTTCCTGGAAGACACGACCCCCGCCAGGGACGAGAAGAAGGTGGGGGCCAAGGCTGCCCAGCAGGACAGCAACAGTGA
TGGGGAGGCCCTGGGCGGCAACCCGATGGTGGCAGGGTTCCAGGACGACGTGGACCTCGAAGACCAGCCACGTGGGAGTC
CCCCGCCGCCCGCGGGCCCCGTCCCCAGTCAAGACATCACTCTTTCGAGTGAGGAAGCAGAAGTGGCGGATCGCCCCAAA
GACCCTGCCCCGGCTCCCCAGCAGTGCTCAGAGCCAGAGACCAAGTGGTCCTCCATACCAGCTTCGAAGCCACGGAGGGG
GACAGCTCCCACGAGGACCGCAGCACCCCCCTGGCCAGGCGGTGCCTCTGTTCGCACAGGTCCGGAGAAGTGCAGCAGCA
CCAGGCCCCCTGCTGAGATTGAGCCAGGGAAGGGTGAGCAGGCCTCTTCGTCGAAGAGTGACCCCGAGGGGCCCATCGCT
GCACAAGTGCTGTCCTTCGTCATGGATGACCCCGACTTTGAGAGCGAGGCATCAGACACACAGCACAGGGCGGATGAGTT
TCCCGTGCGAGATGACCCCTCCGACGTGACTGACGAGGATGAGGCCCCTGCCCAGCCGCCCCCACCCCCCAAGCTCCCTC
TCCCCGCCTTCAGACTGAAGAATGACTCCGACCTCTTTGGGCTGGGGCTGGAGGAGGCCGGACCCAAGGAGAGCAGTGAA
GAAGGTCAGGAGGGCAAAACCCCCTCT

Alignment

ORF - retro_pabe_3577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.65 %
• Parental protein coverage: 89.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFSALKKLVGSDQAPGRDKNIPAGLQSMNQALQRRFAKGVQYNMKIVIRGDRNTGKTALWHRLQGRPFVE
          MFSALKKLVGSDQAPGRDKNIP.GLQSMNQALQRRFAKGVQYNMKIVIRGDRNTGKTALW.RLQGRPFVE
Retrocopy MFSALKKLVGSDQAPGRDKNIPTGLQSMNQALQRRFAKGVQYNMKIVIRGDRNTGKTALWQRLQGRPFVE

Parental  EYIPTQEIQVTSIHWSYKTTDDIVKVEVWDVVDKGKCKKRGDGLKMENDPQEAESEMALDAEFLDVYKNC
          EY.PTQEIQVTSIH.SYKTTDDIVKVEVWDVVDKGKCKKRGDGLKMENDPQEAESEMALDAEFLDVYKNC
Retrocopy EYVPTQEIQVTSIHCSYKTTDDIVKVEVWDVVDKGKCKKRGDGLKMENDPQEAESEMALDAEFLDVYKNC

Parental  NGVVMMFDITKQWTFNYILRELPKVPTHVPVCVLGNYRDMGEHRVILPDDVRDFIDNLDRPPGSSYFRYA
          NGVVMMFDITKQWTFNYIL.ELPKVPTHVPVCVLGNYRDMGEHRVILPDDVRDFIDNLDRPPGSSYFRYA
Retrocopy NGVVMMFDITKQWTFNYILQELPKVPTHVPVCVLGNYRDMGEHRVILPDDVRDFIDNLDRPPGSSYFRYA

Parental  ESSMKNSFGLKYLHKFFNIPFLQLQRETLLRQLETNQLDMDATLEELSVQQETEDQNYGIFLEMMEARSR
          ESSMKNSFGLKYLHKFFNIPFLQLQRETLLRQLETNQLDMD.TLEELSVQQETEDQNYGIFLEMMEARSR
Retrocopy ESSMKNSFGLKYLHKFFNIPFLQLQRETLLRQLETNQLDMDTTLEELSVQQETEDQNYGIFLEMMEARSR

Parental  GHASPLAANGQSPSSGSQSPVVPPGAVSTGSSSPGTPQPAPQLPLNAAPPSSVPP-VPPSEALSPPACPS
          GHASPLAANGQSPSSGSQS.VVPPGAVSTGSSSPGTPQPAPQLPLNAAPPSSVPP.VPPSEAL.P.ACPS
Retrocopy GHASPLAANGQSPSSGSQSTVVPPGAVSTGSSSPGTPQPAPQLPLNAAPPSSVPP<VPPSEALPPSACPS

Parental  APAPRRSIISRLFGTSPAAEAAPPPPEPVPAA-EAPATVQSVEDFVPDDRLDRSFLEDTTPARDEKKVGA
          APAPRRSIISRLFGTSPAAEAAP.PP.....A...P..VQSVEDFVPDDRLDRSFLEDTTPARDEKKVGA
Retrocopy APAPRRSIISRLFGTSPAAEAAP-PPPEPVPA>QRPQQVQSVEDFVPDDRLDRSFLEDTTPARDEKKVGA

Parental  KAAQQDSDSDGEALGGNPMVAGFQDDVDLEDQPRGSPPPPVGPVPSQDITLSSEEEAEVADRPKDPAPAP
          KAAQQDS.SDGEALGGNPMVAGFQDDVDLEDQPRGSPPPP.GPVPSQDITLSSEE.AEVADRPKDPAPAP
Retrocopy KAAQQDSNSDGEALGGNPMVAGFQDDVDLEDQPRGSPPPPAGPVPSQDITLSSEE-AEVADRPKDPAPAP

Parental  QQCSEPETKWSSVPASKPQRGTAPTRTAAPPWPGGASVRTGPEKRSSTRPPAEIEPGKGERASSSESDPE
          QQCSEPETKWSS.PASKP.RGTAPTRTAAPPWPGGASVRTGPEK.SSTRPPAEIEPGKGE.ASSS.SDPE
Retrocopy QQCSEPETKWSSIPASKPRRGTAPTRTAAPPWPGGASVRTGPEKCSSTRPPAEIEPGKGEQASSSKSDPE

Parental  GPIAAQMLSFVMDDPDFESEASDTQHRADEFPVRDDPSDVTDEDEAPAQPPPPPKLPLPAFRLKNDSDLF
          GPIAAQ.LSFVMDDPDFESEASDTQHRADEFPVRDDPSDVTDEDE................RLKNDSDLF
Retrocopy GPIAAQVLSFVMDDPDFESEASDTQHRADEFPVRDDPSDVTDEDEXXXXXXXXXXXXXXXXRLKNDSDLF

Parental  GLGLEEARPKESSEEGKEGKTPS
          GLGLEEA.PKESSEEG.EGKTPS
Retrocopy GLGLEEAGPKESSEEGQEGKTPS

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	1.22 RPM	83.27 RPM
SRP007412_cerebellum	0.73 RPM	46.82 RPM
SRP007412_heart	0.24 RPM	14.87 RPM
SRP007412_kidney	1.23 RPM	42.23 RPM
SRP007412_liver	0.15 RPM	6.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3577 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3577 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	ENSPPYG00000019786	2 retrocopies	retro_pabe_1410, retro_pabe_3577 ,