RetrogeneDB ID: retro_pabe_1410

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16_random:7588288..7590237(+)
• 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_1410
ATGTTTTCCGCCCTGAAGAAGCTGGTGGGGTCGGACCAGGCCCCGGGCCGGGACAAGAACATCCCCACCGGGCTGCAGTC
CATGAACCAGGCGTTGCAGAGGCGTTTCGCCAAGGGGGTGCAGTACAACATGAAGATAGTGATCCGGGGAGACAGGAACA
CGGGCAAAACAGCGCTGTGGCAGCGCCTGCAGGGCCGGCCGTTCGTGGAGGAGTACATCCCCACGCAGGAGATCCAGGTC
ACCAGCATCCACTGGAGCTACAAGACCACGGATGACATCGTGAAGGTTGAAGTCTGGGATGTGGTAGACAAAGGAAAATG
CAAAAAGCGAGGCGGCGGCTTAAAAATGGAGAAGGACCCCCAGGAGGCGGAGTCCGAAATGGCCCTGGATGCTGAGTTCC
TGCACGTGTACAAGAACTGCAACGGGGTGGTCATGATGTTCGATATCACCAAGCAGTGGACCTTCAATTACATTCTCCAG
GAGCTTCCGAAAGTGCCCACCCATGTGCCAGTGTGCGTGCTGGGGAACTACCGGGACATAGGCGAGCACCGAGTCATCCT
GCCGGACGACGTGCGTGACTTCATCGACAACCTGGACAGACCTCCAGGTTCCTCCTACTTCCGCTACGCTGAGTCTTCCA
CGAAGAACAGCTTCGGCCTAAAGTACCTTCATAAGTTCTTCAATATCCCATTTTTGCAGCTTCAGAGGGAGACGCTGTTG
CGGCAGCTGGAGACAAACCAGCTGGACATGGACACCACACTGGAGGAGCTGTCAGTGCAGCAGGAGACGGAGGACCAGAA
CTACGGCATCTTCCTGGAAATGATGGAGGCTCGCAGCCGCGGCCATGCGTCCCCACTGGCGGCCAACGGGCAGAGCCCAT
CCTCGGGCTCCCAGTCAACAGTGGTGCCTCCAGGCGCTGTGTCCACGGGGAGCTCCAGCCCCGGCACACCCCAGCCCGCC
CCACAGCTGCCCCTCAATGCCGCCCCACCATCCTCTGTGCCCCCGTACCACCCTCAGAGGCCCTGCCCCCATCTGCGTGC
CCCTCAGCCCCCGCCCCACGGCGCAGCATCATCTCTAGGCTGTTTGGGACGTCACCTGCTGCCGAGGCAGCCCCTCCACC
TCCAGAGCCAGTCCCGGCCGCAGAGGCCCCAGCAACAGTCCAGAGTGTGGAGGACTTTGTTCCCGATGACCGCCTGGACC
GCAGCTTCCTGGAAGACATGACCCCCGCCAGGGACGAGAAGAAGGTGGGGGCCAAGGCTGCCCAGCAGGACAGCAACAGT
GATGGGGAGGCCCTGGGCGGGAACCCGATGGTGGCAGGGTTCCAGGACGACGTGGACCTCGAAAACCAGCCACGTGGGAG
TCCCCCGCCGCCCGCGGGCCCCGTCCCCAGTCAAGACATCACTCTTTCGAGTGAGGAAGCAGAAGTGGCGGATCGCCCCA
AAGACCCTGCCCCGGCTCCCCAGCAGTGCTCAGAGCCAGAGACCAAGTGGTCCTCCATACCAGCTTCGAAGCCACGGAGG
GGGACAGCTCCCACGAGGACCGCAGCACCCCCCTGGCCAGGCGGTGCCTCTGTTCGCACAGGTCCGGAGAAGCGCAGCAG
CACCAGGCCCCCTGCTGAGATTGAGCCAGGGAAGGGTGAGCAGGCCTCTTCGTTGGAGAGTGACCCCGAGGGGCCCATCG
CTGCACAAATGCTGTCCTTCGTCATGGATGACCCCGACTTTGAGAGCGAGGCATCAGGCACACAGCACAGGGCGGATGAG
TTTCCCGTGCGAGATGACCCCTCCGACGTGACTGACGAAGATGAGGCCCCTGCCCAGCCGCCCCCACCCCCCAAGCTCCC
TCTCCCCGCCTTCAGACTGAAGAATGACTCCGACCTCTTTGGGCTGGGGCTGGAGGAGGCCGGACCCAAGGAGAGCAGTG
AAGAAGGTAAGGAGGGCAAAACCCCCTCT

Alignment

ORF - retro_pabe_1410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.87 %
• Parental protein coverage: 89.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFSALKKLVGSDQAPGRDKNIPAGLQSMNQALQRRFAKGVQYNMKIVIRGDRNTGKTALWHRLQGRPFVE
          MFSALKKLVGSDQAPGRDKNIP.GLQSMNQALQRRFAKGVQYNMKIVIRGDRNTGKTALW.RLQGRPFVE
Retrocopy MFSALKKLVGSDQAPGRDKNIPTGLQSMNQALQRRFAKGVQYNMKIVIRGDRNTGKTALWQRLQGRPFVE

Parental  EYIPTQEIQVTSIHWSYKTTDDIVKVEVWDVVDKGKCKKRGDGLKMENDPQEAESEMALDAEFLDVYKNC
          EYIPTQEIQVTSIHWSYKTTDDIVKVEVWDVVDKGKCKKRG.GLKME.DPQEAESEMALDAEFL.VYKNC
Retrocopy EYIPTQEIQVTSIHWSYKTTDDIVKVEVWDVVDKGKCKKRGGGLKMEKDPQEAESEMALDAEFLHVYKNC

Parental  NGVVMMFDITKQWTFNYILRELPKVPTHVPVCVLGNYRDMGEHRVILPDDVRDFIDNLDRPPGSSYFRYA
          NGVVMMFDITKQWTFNYIL.ELPKVPTHVPVCVLGNYRD.GEHRVILPDDVRDFIDNLDRPPGSSYFRYA
Retrocopy NGVVMMFDITKQWTFNYILQELPKVPTHVPVCVLGNYRDIGEHRVILPDDVRDFIDNLDRPPGSSYFRYA

Parental  ESSMKNSFGLKYLHKFFNIPFLQLQRETLLRQLETNQLDMDATLEELSVQQETEDQNYGIFLEMMEARSR
          ESS.KNSFGLKYLHKFFNIPFLQLQRETLLRQLETNQLDMD.TLEELSVQQETEDQNYGIFLEMMEARSR
Retrocopy ESSTKNSFGLKYLHKFFNIPFLQLQRETLLRQLETNQLDMDTTLEELSVQQETEDQNYGIFLEMMEARSR

Parental  GHASPLAANGQSPSSGSQSPVVPPGAVSTGSSSPGTPQPAPQLPLNAAPPSSVP-PVPPSEALSPPACPS
          GHASPLAANGQSPSSGSQS.VVPPGAVSTGSSSPGTPQPAPQLPLNAAPPSSVP.PVPPSEAL.P.ACPS
Retrocopy GHASPLAANGQSPSSGSQSTVVPPGAVSTGSSSPGTPQPAPQLPLNAAPPSSVP<PVPPSEALPPSACPS

Parental  APAPRRSIISRLFGTSPAAEAAPPPPEPVPAAEAPATVQSVEDFVPDDRLDRSFLEDTTPARDEKKVGAK
          APAPRRSIISRLFGTSPAAEAAPPPPEPVPAAEAPATVQSVEDFVPDDRLDRSFLED.TPARDEKKVGAK
Retrocopy APAPRRSIISRLFGTSPAAEAAPPPPEPVPAAEAPATVQSVEDFVPDDRLDRSFLEDMTPARDEKKVGAK

Parental  AAQQDSDSDGEALGGNPMVAGFQDDVDLEDQPRGSPPPPVGPVPSQDITLSSEEEAEVADRPKDPAPAPQ
          AAQQDS.SDGEALGGNPMVAGFQDDVDLE.QPRGSPPPP.GPVPSQDITLSS.EEAEVADRPKDPAPAPQ
Retrocopy AAQQDSNSDGEALGGNPMVAGFQDDVDLENQPRGSPPPPAGPVPSQDITLSS-EEAEVADRPKDPAPAPQ

Parental  QCSEPETKWSSVPASKPQRGTAPTRTAAPPWPGGASVRTGPEKRSSTRPPAEIEPGKGERASSSESDPEG
          QCSEPETKWSS.PASKP.RGTAPTRTAAPPWPGGASVRTGPEKRSSTRPPAEIEPGKGE.ASS.ESDPEG
Retrocopy QCSEPETKWSSIPASKPRRGTAPTRTAAPPWPGGASVRTGPEKRSSTRPPAEIEPGKGEQASSLESDPEG

Parental  PIAAQMLSFVMDDPDFESEASDTQHRADEFPVRDDPSDVTDEDEAPAQPPPPPKLPLPAFRLKNDSDLFG
          PIAAQMLSFVMDDPDFESEAS.TQHRADEFPVRDDPSDVTDEDE................RLKNDSDLFG
Retrocopy PIAAQMLSFVMDDPDFESEASGTQHRADEFPVRDDPSDVTDEDEXXXXXXXXXXXXXXXXRLKNDSDLFG

Parental  LGLEEARPKESSEEGKEGKTPS
          LGLEEA.PKESSEEGKEGKTPS
Retrocopy LGLEEAGPKESSEEGKEGKTPS

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	83.27 RPM
SRP007412_cerebellum	0.24 RPM	46.82 RPM
SRP007412_heart	0.06 RPM	14.87 RPM
SRP007412_kidney	0.13 RPM	42.23 RPM
SRP007412_liver	0.06 RPM	6.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1410 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1410 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1410 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,