RetrogeneDB ID: retro_tbel_4481

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_85149:3256..4135(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPP1
• Ensembl ID: ENSTBEG00000011524
• Aliases: None
• Description: membrane protein, palmitoylated 1, 55kDa [Source:HGNC Symbol;Acc:7219]

Sequence

>retro_tbel_4481
GCTGTGTCACACCAGCTGAATGCTGTGACCGAAGACATGTACACCAATGGGTCTGCTGCCCCAGGTAGTCCTGCCCAATG
CAAAGGACAGGAGCTGCGAAAAGTGCGCCTCATACAATTTGAGAAGGTCACAGAGGAGGAGCCCATGGGAATCACTCTGA
AGCTGAATGAAAAACAGTCCTGTACAGTGGCCAGAATTCTTCATGGTGGCATGATCCATAGACAAGGCTCCCTTCATGTG
GGGGATGAGATCCTAGAAATCAATGGCACAAATGTGACTAATCACTCCGTAGATCAGCTGCAGAAGGCAATGAAAGAAAC
AAAAGGAATGATCTCAATAAAAGTAATTCCCAACCAGCAAAGCCGTCTTCCTGCACTACTGATGTTCATGAGAGTGCAAT
TTGACTATGATCCCCAAAAGGACAGCCTGATCCCTTGTAAGGAGGCAGGGCTGAAGTTCGCTACTGGGGACCTTATTCAG
ATCATCAACAAGGATGACAGCAACTGGTGGCAGGGACTGGTGGAAGGCTCCTCCAAGGAGTCAGCAGGACTGATCCCCTC
CCCCGAACTGCAGGAGTGACAAGTGGCAAGTGTGGTTCAGTCTGCTCCGAGTGAAGCCCCAAGCTGCAGTCCCTTCAGAA
AGAAGAAGTACAAAGACAAGTACCTGGCCAAGCACAGCTCGATTTTTGACCAGTTGGATGTCATTTCCTATGAGGAAGTT
GTCCGGCTCCCTGCATTCAAAAGGAAGACCCTGGTGCTGATCGGAGCCAGTGGGGTGGGTCGCAGCCACATCAAGAATGC
CCTGCTCAGCCAGAATCCAGAGAAGTTTGTGTACCCTGCCCCATATACAACACGACCATCAAGGAAGAGTGAGGAAGAT

Alignment

ORF - retro_tbel_4481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.58 %
• Parental protein coverage: 67.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVSHQLNAVTEDMYTNGSAAPGSPAQSKGQELRKVRLIQFEKVT-EEPMGITLKLNEKQSCTVARILHGG
          AVSHQLNAVTEDMYTNGSAAPGSPAQ.KGQELRKVRLIQFEKVT.EEPMGITLKLNEKQSCTVARILHGG
Retrocopy AVSHQLNAVTEDMYTNGSAAPGSPAQCKGQELRKVRLIQFEKVTEEEPMGITLKLNEKQSCTVARILHGG

Parental  MIHRQGSLHVGDEILEINGTNVTNHSVDQLQKAMKETKGMISLKVIPNQQSRLPALQMFMRAQFDYDPQK
          MIHRQGSLHVGDEILEINGTNVTNHSVDQLQKAMKETKGMIS.KVIPNQQSRLPAL.MFMR.QFDYDPQK
Retrocopy MIHRQGSLHVGDEILEINGTNVTNHSVDQLQKAMKETKGMISIKVIPNQQSRLPALLMFMRVQFDYDPQK

Parental  DSLIPCKEAGLKFATGDIIQIINKDDSNWWQGRVEGSSKESAGLIPSPELQEWRVASVAQSAPSEAPSCS
          DSLIPCKEAGLKFATGD.IQIINKDDSNWWQG.VEGSSKESAGLIPSPELQE..VASV.QSAPSEAPSCS
Retrocopy DSLIPCKEAGLKFATGDLIQIINKDDSNWWQGLVEGSSKESAGLIPSPELQE*QVASVVQSAPSEAPSCS

Parental  PFGKKKKYKDKYLAKHSSIFDQLDVISYEEVVRLPAFKRKTLVLIGASGVGRSHIKNALLSQNPEKFVYP
          PF..KKKYKDKYLAKHSSIFDQLDVISYEEVVRLPAFKRKTLVLIGASGVGRSHIKNALLSQNPEKFVYP
Retrocopy PF-RKKKYKDKYLAKHSSIFDQLDVISYEEVVRLPAFKRKTLVLIGASGVGRSHIKNALLSQNPEKFVYP

Parental  APYTTRPPRKSEED
          APYTTRP.RKSEED
Retrocopy APYTTRPSRKSEED

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_4481 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4481 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004231	1 retrocopy	retro_dnov_977,
Felis catus	ENSFCAG00000006578	1 retrocopy	retro_fcat_1352,
Pteropus vampyrus	ENSPVAG00000009226	1 retrocopy	retro_pvam_709,
Tupaia belangeri	ENSTBEG00000011524	2 retrocopies	retro_tbel_4481 , retro_tbel_564,