RetrogeneDB ID: retro_tbel_4490

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_85505:5199..6375(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000011602
• Aliases: None
• Description: None

Sequence

>retro_tbel_4490
AACGTGCTGATCTTTGACTTGGGAGGTGGCACTTTTGATGTGTCCATCCTCACTATTGAGGATGGGATTTTTGAGGTCAA
ATCTACAGCTGGAGATACACACTTGGGCGGAGAAGACTTCGACAATCGCATGGTCAACCATTTCATCGCCAAGTTTAAGC
GCAGGCATAAGAAGGACATCAGTGAGAACAAGAGAGCTGTCCGCCACCTTCGCACTGCTTGGGAACAGGCTAAATGCACC
CACTCCTCCAGCACCCAGGCCAATATTGAGATCAACTCCCTCTATGAAGGAATCGACTTCTATACCTCCATTACCCGTGC
CCAATTTGAAGAGTTGAATGCAGACCTGTTCCATGGGACCCTGGACCCTGTAGAAAAAGCCCTTCGGGATGCTAAACTAG
ACAAGTCACAGATCCATGACATTGTCCTGGTGGGTGGCTCTACTCGTATCCCCAAGATTCAGAAGCTGCTGCAAGGCTTC
TTCAACGGGAAAGAACTGAATAAGAGCATCAACCCTGATGAGGCCGTTGCTTATGGAGCAGCTGTCCAGGCAGCCATCTT
ATCTGGAGACAAGTCTGAGAACGTTCAGAACCTGCTGCTCTTGGATGTCACGCCTCTGTCCCTCGGCATCGAAACTGCTG
GCGCGGTCATGACTGTCCTCATCAAACGGAACATCACCATTCCCACCAAGCAGACACAGACCTTCACCACCTACTCCGAC
AACCAGCCCGGGGTGCTCATCCAGGTTTATGAAAGTGAGCGCGCCATGACCAAGGATAACAACCTGCTGGGCGAGGTTGA
GCTCACAGGCATACCTCCTGCACCCCGTGGTGTTCCTCAGATTGAAGTCACTTTCGACATCGGTGCCAATGGCATCCTGA
ACGTCTCTGCTGTGGATAAGAGTATCGGGAAAGAGAACAAGATCACCATCGCCAACGATAAGGGTCACCTGAGCAAGGAG
GGCATCGAGCTCATGGTCCAGGAGGCTAAGAAGTACAAGGTTGAGGACGAGAAGCAAAGGGACAAGGTGCCTTCCAAGAA
CTCCCTGGAGTTCTACGCATTCAACATGAAAGCCATGGTGAAGGACAAGAAACTCCAAGGCAAGATTAATAATGAGGACA
AGCAGAAGATTCATGACAAATATAATAAAATCATCAACTGGCTTGACAAGAACCAG

Alignment

ORF - retro_tbel_4490 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.07 %
• Parental protein coverage: 67.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRL
          NVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIA.FKR.HKKDISENKRAVR.L
Retrocopy NVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAKFKRRHKKDISENKRAVRHL

Parental  RTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHD
          RTA.E.AK.T.SSSTQA.IEI.SLYEGIDFYTSITRA.FEELNADLF.GTLDPVEKALRDAKLDKSQIHD
Retrocopy RTAWEQAKCTHSSSTQANIEINSLYEGIDFYTSITRAQFEELNADLFHGTLDPVEKALRDAKLDKSQIHD

Parental  IVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGI
          IVLVGGSTRIPKIQKLLQ.FFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQ.LLLLDVTPLSLGI
Retrocopy IVLVGGSTRIPKIQKLLQGFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQNLLLLDVTPLSLGI

Parental  ETAGGVMTVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQ
          ETAG.VMTVLIKRN.TIPTKQTQTFTTYSDNQPGVLIQVYE.ERAMTKDNNLLG..ELTGIPPAPRGVPQ
Retrocopy ETAGAVMTVLIKRNITIPTKQTQTFTTYSDNQPGVLIQVYESERAMTKDNNLLGEVELTGIPPAPRGVPQ

Parental  IEVTFDIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLE
          IEVTFDI.ANGILNVSAVDKS.GKENKITI.NDKG.LSKE.IE.MVQEA.KYK.EDEKQRDKV.SKNSLE
Retrocopy IEVTFDIGANGILNVSAVDKSIGKENKITIANDKGHLSKEGIELMVQEAKKYKVEDEKQRDKVPSKNSLE

Parental  SYAFNMKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQ
          .YAFNMKA.V.D.KLQGKIN.EDKQKI.DK.N.IINWLDKNQ
Retrocopy FYAFNMKAMVKDKKLQGKINNEDKQKIHDKYNKIINWLDKNQ

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_4490 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4490 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000012704	1 retrocopy	retro_eeur_8,
Microcebus murinus	ENSMICG00000004702	1 retrocopy	retro_mmur_7,
Sorex araneus	ENSSARG00000000161	1 retrocopy	retro_sara_31,
Tupaia belangeri	ENSTBEG00000011602	8 retrocopies	retro_tbel_1764, retro_tbel_344, retro_tbel_3488, retro_tbel_3524, retro_tbel_4348, retro_tbel_4412, retro_tbel_4490 , retro_tbel_471,