RetrogeneDB ID: retro_pabe_3190

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:140902054..140903563(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNB1
• Ensembl ID: ENSPPYG00000025935
• Aliases: None
• Description: karyopherin (importin) beta 1 [Source:HGNC Symbol;Acc:6400]

Sequence

>retro_pabe_3190
GAAATGGATTTGGCAGCAGAACAAGGACGGCCCCCTGAGCACACCAGCAAGTTTTATGCCAAGGGAGCACTACAGTATCT
GGTTCCAATCCTCATACAGACACTAACTAAACAGGATGAAAATGATGATGACGATGACTGGAACCCCTGCAAAGCAGCAG
GGGTGTGCCTCATGCTTCTGGCCACCTGCTGTGAAGATGACATTGTCCCACATGTCCTCCCCTTCATTAAAGAACACATC
AAGAACCCAGACTGGCGGTACCGGGATGCAGCAGTGATGGCTTTTGGTTGTATCTTGGAACGACCAGAGCCCAGTTAGCT
CAAACCACTAGTTATACAGGCTATGCCCACCCTAATAGAATTAATGAAAGACCCCAGTGTAGTTGTTCGAGATACAGCTG
CATGGACTGTAGGCAGAATTTGTGAGCTGCTTCCTGAAGCTGCCATCAATGATGTCTACTTGGCTCTCCTGCTACAGTGT
CTGATTGAGGGTCTCAGTGCTGAACCCAGAGTGGCTTCAAATGTGTGCTGGGCTTTCTCCAGTCTGGCTGAAGCTGCTTA
TGAAGCTGCAGACATTGCTGATGATCAGGAAGAACCAGCTACTTACTGCTTGTCTTCTTCATTTGAACTTATAGTTCAGA
AGCTCCTAGAGACTACAGACAGACCTGATGGACATCAGAACAACCTGAGGAGTTCTGCATATGAATCTCTGATGGAAATT
GTGAAAAACAGTGCCAAGGATTGTTATCCTGCTGTCCAGAAAACGACTTTGGTCATCATGGAACGACTGCAACAGGTTCT
TCAGATGGAGTCACATATCCAGAGCACATCCGATAGAATCCAGTTCAATGACCTTCAGTCTTTACTCTGTGCAACTCTTC
AGAATGTTCTTCGGAAAGTGCAACATCAAGATGCTTTGCAGATCTCTGATGTGGTTATGGCCTCCCTGTTAAGGATGTTC
CAAAGCACAGCTGGGTCTGGGGGAGTACAAGAAGATGCCCTGATGGCAGTTAGCACACTGGTGGAAGTGTTGGGTGGTGA
ATTCCTCAAGTACATGGAGGCCTTTAAACCCTTCCTGGGCATTGGATTAAGAAATTATGCTCAGTACCAGGTTTGTTTGG
CAGCTGTGGGCTTAGTGGGAGACTTGTGCCGTGCCCTGCAATCCAACATCATACCTTTCTGTGACGAGGTGATGCAGCTG
CTTCTGGAAAATTTGGGGAATGAGAACGTCCACAGGTCTGTGAAGCCGCAGATTCTGTCAGTGTTTGGTGATATTGCCCT
TGCTATTGGTGGAGAGTTTAAAAAATACTTAGAGGTTGTATTGAATACTCTTCAGCAGGCCTCCCAAGCCCAGGTGGACA
AGTCAGACTATGACATCATGGATTATCTGAATGAGCTAAGGGAAAGCTGCTTGGAAGCCTATACCGGAATCGTCCAGGGA
TTAAAGGGGGATCGGGAGAACGTACACCCGGATGTGATGCTGGTACAACCCAGAGTAGAATTTATTCTC

Alignment

ORF - retro_pabe_3190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.42 %
• Parental protein coverage: 68.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EASEAAEQGRPPEHTSKFYAKGALQYLVPILTQTLTKQDENDDDDDWNPCKAAGVCLMLLATCCEDDIVP
          E...AAEQGRPPEHTSKFYAKGALQYLVPIL.QTLTKQDENDDDDDWNPCKAAGVCLMLLATCCEDDIVP
Retrocopy EMDLAAEQGRPPEHTSKFYAKGALQYLVPILIQTLTKQDENDDDDDWNPCKAAGVCLMLLATCCEDDIVP

Parental  HVLPFIKEHIKNPDWRYRDAAVMAFGCILEGPEPSQLKPLVIQAMPTLIELMKDPSVVVRDTAAWTVGRI
          HVLPFIKEHIKNPDWRYRDAAVMAFGCILE.PEPS.LKPLVIQAMPTLIELMKDPSVVVRDTAAWTVGRI
Retrocopy HVLPFIKEHIKNPDWRYRDAAVMAFGCILERPEPS*LKPLVIQAMPTLIELMKDPSVVVRDTAAWTVGRI

Parental  CELLPEAAINDVYLAPLLQCLIEGLSAEPRVASNVCWAFSSLAEAAYEAADVADDQEEPATYCLSSSFEL
          CELLPEAAINDVYLA.LLQCLIEGLSAEPRVASNVCWAFSSLAEAAYEAAD.ADDQEEPATYCLSSSFEL
Retrocopy CELLPEAAINDVYLALLLQCLIEGLSAEPRVASNVCWAFSSLAEAAYEAADIADDQEEPATYCLSSSFEL

Parental  IVQKLLETTDRPDGHQNNLRSSAYESLMEIVKNSAKDCYPAVQKTTLVIMERLQQVLQMESHIQSTSDRI
          IVQKLLETTDRPDGHQNNLRSSAYESLMEIVKNSAKDCYPAVQKTTLVIMERLQQVLQMESHIQSTSDRI
Retrocopy IVQKLLETTDRPDGHQNNLRSSAYESLMEIVKNSAKDCYPAVQKTTLVIMERLQQVLQMESHIQSTSDRI

Parental  QFNDLQSLLCATLQNVLRKVQHQDALQISDVVMASLLRMFQSTAGSGGVQEDALMAVSTLVEVLGGEFLK
          QFNDLQSLLCATLQNVLRKVQHQDALQISDVVMASLLRMFQSTAGSGGVQEDALMAVSTLVEVLGGEFLK
Retrocopy QFNDLQSLLCATLQNVLRKVQHQDALQISDVVMASLLRMFQSTAGSGGVQEDALMAVSTLVEVLGGEFLK

Parental  YMEAFKPFLGIGLKNYAEYQVCLAAVGLVGDLCRALQSNIIPFCDEVMQLLLENLGNENVHRSVKPQILS
          YMEAFKPFLGIGL.NYA.YQVCLAAVGLVGDLCRALQSNIIPFCDEVMQLLLENLGNENVHRSVKPQILS
Retrocopy YMEAFKPFLGIGLRNYAQYQVCLAAVGLVGDLCRALQSNIIPFCDEVMQLLLENLGNENVHRSVKPQILS

Parental  VFGDIALAIGGEFKKYLEVVLNTLQQASQAQVDKSDYDMVDYLNELRESCLEAYTGIVQGLKGDQENVHP
          VFGDIALAIGGEFKKYLEVVLNTLQQASQAQVDKSDYD..DYLNELRESCLEAYTGIVQGLKGD.ENVHP
Retrocopy VFGDIALAIGGEFKKYLEVVLNTLQQASQAQVDKSDYDIMDYLNELRESCLEAYTGIVQGLKGDRENVHP

Parental  DVMLVQPRVEFIL
          DVMLVQPRVEFIL
Retrocopy DVMLVQPRVEFIL

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	0.33 RPM	108.20 RPM
SRP007412_cerebellum	0.36 RPM	87.67 RPM
SRP007412_heart	0.15 RPM	58.79 RPM
SRP007412_kidney	0.17 RPM	91.85 RPM
SRP007412_liver	0.03 RPM	51.84 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3190 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3190 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3190 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000025935	1 retrocopy	retro_pabe_3190 ,