RetrogeneDB ID: retro_tbel_2180

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_103773:2942..3799(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNDC15
• Ensembl ID: ENSTBEG00000015609
• Aliases: None
• Description: thioredoxin domain containing 15 [Source:HGNC Symbol;Acc:20652]

Sequence

>retro_tbel_2180
GCAGAAGAGGCTGAAGCAGTGCTGGGGCTGGACAGCCCTGGTGGTCACATGGTGATGTTGTCTGTGATTCCCGGGGAAGC
TGAGAACAAACTGAGCTCAGAGCCTAGCAGCGGCACCTGTGGCGCTGGCGGAAAGGACTCAAGGTGCCACCTTCGAGAGA
GCCTCTTCTCTCTGTACAGTGCTGGCGCCAGCTTCCCTGATAGGGAAGAGGAGTGTTACACAGAGCCAGAAGTGGCAGAA
ACCGACCTGGCACCGACAGAGGACTCCGATAGCACCGAAAGCCTGAAGTCCCCCAAGGTCAGCTGTGAGGAGAGAAATGT
GACAGGACTGAAAATTTTCACCCTGAAAATTCTAAATATGTCACAAGACCTCATGGATTTTCTAAACCCAAATGGCAGTG
ACTATACTCTGGTTCTGTTTTACACCCCGTGGTGACGGTTTTCTGCCAGTTTGGCCCCTCACTTTAATTCACTGCCTCAG
GCATTTCCAGCTCTTCACTTTTAGGTCCTGGACGCATCTCAGAACAGCAGCCTTTCTACCAGGTTTTGGCACCGTAGCGG
TTCCTAACATTTTGTTATTTCAAGGAGTGAAACCAATGGCTAGGTTTTAATCATACAGATCAAACATTGGAAACGCTGAA
AATCTTCATTTTTAATCAGACAGGTATAGAAGCCAAGAAAAATGTGGTGGTAACTCAAGCTGACCCAATAGGTCCTCTTC
CCAGCACTTTGATAAAAAGTGTGGACTGGCTGCTTGTATTTTTCTTATTCTTTTAAATTAGTTTTATTATGTATGCTACC
ATTTGAATGGAGAGTATTCAGTGGCTAATTCCAGGACAAGAGCAGGAACACGTGGAA

Alignment

ORF - retro_tbel_2180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.38 %
• Parental protein coverage: 79.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AEEAEAVLGLDSPGGHMVMLSVIPGEAENKLSSEPSSGTCGAGGKDSRCHLRESLFSLYSAGASFPDREE
          AEEAEAVLGLDSPGGHMVMLSVIPGEAENKLSSEPSSGTCGAGGKDSRCHLRESLFSLYSAGASFPDREE
Retrocopy AEEAEAVLGLDSPGGHMVMLSVIPGEAENKLSSEPSSGTCGAGGKDSRCHLRESLFSLYSAGASFPDREE

Parental  ECYTEPEVAETDLAPTEDSDSTESLKSPKVSCEERNVTGLKIFTLKILNMSQDLMDFLNPNGSDCTLVLF
          ECYTEPEVAETDLAPTEDSDSTESLKSPKVSCEERNVTGLKIFTLKILNMSQDLMDFLNPNGSD.TLVLF
Retrocopy ECYTEPEVAETDLAPTEDSDSTESLKSPKVSCEERNVTGLKIFTLKILNMSQDLMDFLNPNGSDYTLVLF

Parental  YTPWCRFSASLAPHFNSLPRAFPALHFLALDASQHSSLSTR-FGTVAVPNI-LFQGSEPMAR-FNHTDRT
          YTPW.RFSASLAPHFNSLP.AFPALHF..LDASQ.SSLSTR.FGTVAVPNI.LFQG..PMAR.FNHTD.T
Retrocopy YTPW*RFSASLAPHFNSLPQAFPALHF*VLDASQNSSLSTR>FGTVAVPNILLFQGVKPMAR>FNHTDQT

Parental  LETLK-FIFNQTGIEAKKNVVVTQADQIGPLPSTLIKSVDWLLVFSLFFLISFIMYATIRTESIRWLIPG
          LETLK.FIFNQTGIEAKKNVVVTQAD.IGPLPSTLIKSVDWLLVF.LFF.ISFIMYATI..ESI.WLIPG
Retrocopy LETLKIFIFNQTGIEAKKNVVVTQADPIGPLPSTLIKSVDWLLVFFLFF*ISFIMYATI*MESIQWLIPG

Parental  QEQEHVE
          QEQEHVE
Retrocopy QEQEHVE

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_2180 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2180 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000014348	3 retrocopies	retro_mdom_1644, retro_mdom_646, retro_mdom_759,
Tupaia belangeri	ENSTBEG00000015609	1 retrocopy	retro_tbel_2180 ,