RetrogeneDB ID: retro_tbel_4256

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_73453:131..1539(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPR
• Ensembl ID: ENSTBEG00000002251
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein R [Source:HGNC Symbol;Acc:5047]

Sequence

>retro_tbel_4256
TTTGTAGGTAAAATTCCAAGAGATTTATATGAAGATGAGTTGGTGCCTCTTTTTGAGAAGGCTGGTCCCATTTGGGATCT
GCATCTTATGATGGATCCACTATCTGGTCAGAATAGAGGGTATGCATTTATCACCTTCTGTGGAAAGGAAGCTGCACAGG
AAGCTGTTAAACTGTGTGACAGCTATGAAATTCGCCCTGGTAAATACCTTGGAGTGTGCATTTCTGTGGCAAACAACAGG
CTTTTTGTTGGATCCATTCCAAAGAATAAGACTAAAGAAAACATTCTGGAAGAATTCAGTAAAGTCACAGGTTTAACAGA
GGGTTTGGTGGACGTTATTCTCTATCATCAACCCAATGACAAAAAGAAGAATCGGGGGTTCTGCTTCCTTGAATATGAGG
ATCACAAGTCAGCAACACAAGCCAGACGCCGGCTGATGAGTGGAAAAGTAAAAGTGTGGGGAAATGTAGTTACAGTTGAA
TGGGCTGACCCTGTGGAAGAACCAGATCCAGAAGTCATGGCTAAGGTGAAAGTTTTATTTGTGAGAAACTTGGCTACTAC
AGTGATGGAAGAAATATTGGAAAAGTCATTTTCTGAATTTGGAAAACTTGAAAGAGTAAAGAAGTTGAAAGATTATGCAT
TTGTTCATTTTGAAGACAGAGGAGCAGCTGTTAAGGCTATGGATGAAACGAATGGCAAAGAAATATAAGGGGAAGAAATT
GAAATTGTCTTAGCCAAGCCAACGGACAAGAAAAGGAAAGAGCGCCAAGCTGCTAGACAGGCCTCCAGAAGCACTGCGTA
TGAAGATTATTACTATCACCCTCCTCCTCGCATGCCACCTCCCAATTAGAGGTCGGGGTCGTGGTGGGGGGAGAGGTGGA
TATGGCTACCCTCCAGATTACTATGGCTATGAAGATTACTATGATGATTACTATGGTTACGATTATCATGACTATTGTGG
AGGCTATGAAGACCCCTACTACGGCTATGATGATGGCTATGCAGTAAGAGGAAGAGGAGGAGGAAGGGGAGGGCGAGGTG
CTCCACCACCACCAAGGGGGTGGGGAGCACCACCTCCAAGAAGTAGAGCTGGCTATTCACAAAGGGGGGCACCCTTGGGA
TCACCAAGAGGTTCTAGGGGTGGCAGAGGGGGTCCTGCACAACAGCAGAGAGGCCGTGGTTCTCGTGGATCTCGGGGCAA
TCATGGGGGCAATGTAGGAGGCAAGAGAAAGGCAGATGGGTACAACCAACCTGATTCTAAGTGTCGTCAGACCAACAACC
AACAGAACTGGGGTTCCCAACCCATCGCTCAGCAGCCGCTTCAGCAAGGTGGTGACTATTCTGGCAACTATGGTTATAAT
AATGACAACCAGGAATTTTATCAGGATACTTATAGGCAACAATGGAAA

Alignment

ORF - retro_tbel_4256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.49 %
• Parental protein coverage: 73.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLCDSYEIRPGKHL
          FVGKIPRDLYEDELVPLFEKAGPIWDL.LMMDPLSGQNRGYAFITFCGKEAAQEAVKLCDSYEIRPGK.L
Retrocopy FVGKIPRDLYEDELVPLFEKAGPIWDLHLMMDPLSGQNRGYAFITFCGKEAAQEAVKLCDSYEIRPGKYL

Parental  GVCISVANNRLFVGSIPKNKTKENILEEFSKVTGLTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQ
          GVCISVANNRLFVGSIPKNKTKENILEEFSKVTGLTEGLVDVILYHQP.DKKKNRGFCFLEYEDHKSA.Q
Retrocopy GVCISVANNRLFVGSIPKNKTKENILEEFSKVTGLTEGLVDVILYHQPNDKKKNRGFCFLEYEDHKSATQ

Parental  ARRRLMSGKVKVWGNVVTVEWADPVEEPDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLK
          ARRRLMSGKVKVWGNVVTVEWADPVEEPDPEVMAKVKVLFVRNLATTV.EEILEKSFSEFGKLERVKKLK
Retrocopy ARRRLMSGKVKVWGNVVTVEWADPVEEPDPEVMAKVKVLFVRNLATTVMEEILEKSFSEFGKLERVKKLK

Parental  DYAFVHFEDRGAAVKAMDEMNGKEIEGEEIEIVLAKPPDKKRKERQAARQASRSTAYEDYYYHPPPRMPP
          DYAFVHFEDRGAAVKAMDE.NGKEI.GEEIEIVLAKP.DKKRKERQAARQASRSTAYEDYYYHPPPRMPP
Retrocopy DYAFVHFEDRGAAVKAMDETNGKEI*GEEIEIVLAKPTDKKRKERQAARQASRSTAYEDYYYHPPPRMPP

Parental  -PIRGRGRGGGRGGYGYPPDYYGYEDYYDDYYGYDYHDYRGGYEDPYYGYDDGYAVRGRGGGRGGRGAPP
          .PIRGRGRGGGRGGYGYPPDYY...........YDYHDY.GGYEDPYYGYDDGY.............APP
Retrocopy >PIRGRGRGGGRGGYGYPPDYYXXXXXXXXXXXYDYHDYCGGYEDPYYGYDDGYXXXXXXXXXXXXXAPP

Parental  PPRGRGAPPPRGRAGYSQRGAPLGPPRGSRGGRGGPAQQQRGRGSRGSRGNRGGNVGGKRKADGYNQPDS
          PPRG.GAPPPR.RAGYSQRGAPLG.PRGSRGGRGGPAQQQRGRGSRGSRGN.GGNVGGKRKADGYNQPDS
Retrocopy PPRGWGAPPPRSRAGYSQRGAPLGSPRGSRGGRGGPAQQQRGRGSRGSRGNHGGNVGGKRKADGYNQPDS

Parental  KRRQTNNQQNWGSQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTYGQQWK
          K.RQTNNQQNWGSQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTY.QQWK
Retrocopy KCRQTNNQQNWGSQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTYRQQWK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4256 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4256 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000125944	1 retrocopy	retro_hsap_651,
Gorilla gorilla	ENSGGOG00000013250	1 retrocopy	retro_ggor_568,
Macaca mulatta	ENSMMUG00000010970	1 retrocopy	retro_mmul_2433,
Monodelphis domestica	ENSMODG00000016144	1 retrocopy	retro_mdom_240,
Mus musculus	ENSMUSG00000066037	1 retrocopy	retro_mmus_458,
Otolemur garnettii	ENSOGAG00000009179	1 retrocopy	retro_ogar_3144,
Procavia capensis	ENSPCAG00000010462	1 retrocopy	retro_pcap_88,
Pan troglodytes	ENSPTRG00000000324	1 retrocopy	retro_ptro_474,
Tupaia belangeri	ENSTBEG00000002251	1 retrocopy	retro_tbel_4256 ,