RetrogeneDB ID: retro_tbel_2021

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_705:114591..115292(+)
• Located in intron of: ENSTBEG00000001936

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLIC5
• Ensembl ID: ENSTBEG00000007344
• Aliases: None
• Description: chloride intracellular channel 5 [Source:HGNC Symbol;Acc:13517]

Sequence

>retro_tbel_2021
CCACGGGTCGAATTGTTCATGAAGGCTGGCAGTGATGGGGCCAAGATTGGAAACTGTCCCTTCTCCCAGAGACTGTTCAT
GGTGCTCTGGCTCAAGGGAGTCACCTTCAATGTCATCACCGTTGACACCAAGAGACGGACGGAGACGGTGCAGAAGCTGT
GCCCAGGAGGGCAGCTCCCATTCCTGCTCTATGGCACCGAGGTGCACACAACACCAACAAGATTGATGAATTTCTGGAAG
CAGTGCTGTGCCCTCCCAGGTACCCCAAACTGGCAGCTCTGAACCCTGAGTCTAACACAGCTGGGCTGGACATATTTGCC
AAATTTTCTGCCTACATCAAGAATTCAAACCTAGCTCTCAATGATAATCTGGAGAAAGGACTTCTGAAAGCCCTGAAGGT
TTTAGACAATTACTTGACCACTCCTCTCCCAGAAGTGGATGAGACCAGTGCTGAAGATGAAGGTGTTTCTCAGAGGAAAT
TTCTGCATGGCAACGAGCTCACTTTGGCTGCCTCCAACCTGCTGCCAAAGCTCCACGTAGTGCAGGTGGTGTGTAAGAAA
TATCGGGGCTTCACCATCCCAGAAGCCTTTCGGGGAGTTCATCGGTACTTAAGCAATGCCTATGCTCAGGAAGAATTCGC
CTGTACGTGTCCAGGTGACAAGGAGATTGAACTGGCCTATGAGCAAGTGGCCAACGCCCTC

Alignment

ORF - retro_tbel_2021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.76 %
• Parental protein coverage: 57.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PDISLFVKAGIDGESIGNCPFSQRLFMILWLKGVVFNVTTVDLKRKPADLHNLAPGTHPPFLTFNGDVKT
          P...LF.KAG.DG..IGNCPFSQRLFM.LWLKGV.FNV.TVD.KR.......L.PG...PFL.....V.T
Retrocopy PRVELFMKAGSDGAKIGNCPFSQRLFMVLWLKGVTFNVITVDTKRRTETVQKLCPGGQLPFLLYGTEVHT

Parental  -DVNKIEEFLEETLTPEKYPKLAAKHRESNTAGIDIFSKFSAYIKNTKQQNNAALERGLTKALKKLDDYL
          ...NKI.EFLE..L.P..YPKLAA...ESNTAG.DIF.KFSAYIKN.....N..LE.GL.KALK.LD.YL
Retrocopy <NTNKIDEFLEAVLCPPRYPKLAALNPESNTAGLDIFAKFSAYIKNSNLALNDNLEKGLLKALKVLDNYL

Parental  NTPLPEEIDANTCGDDDKGSQRKFLDGDELTLADCNLLPKLHVVKIVAKKYRNYDLPAEMTGLRRYLKNA
          .TPLPE..D..T...D...SQRKFL.G.ELTLA..NLLPKLHVV..V.KKYR....P....G..RYL.NA
Retrocopy TTPLPE-VD-ETSAEDEGVSQRKFLHGNELTLAASNLLPKLHVVQVVCKKYRGFTIPEAFRGVHRYLSNA

Parental  YARDEFTNTCAADQEIELAYADVAKRL
          YA..EF..TC..D.EIELAY..VA..L
Retrocopy YAQEEFACTCPGDKEIELAYEQVANAL

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_2021 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2021 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000006075	1 retrocopy	retro_pvam_901,
Tupaia belangeri	ENSTBEG00000007344	1 retrocopy	retro_tbel_2021 ,