RetrogeneDB ID: retro_tbel_3522

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_143685:7713..8240(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000009521
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GCLM
• Ensembl ID: ENSTBEG00000006631
• Aliases: None
• Description: glutamate-cysteine ligase, modifier subunit [Source:HGNC Symbol;Acc:4312]

Sequence

>retro_tbel_3522
CTTAGATATTGTATTCAAAAGACCTTGAATAAGTGGAGTTCCCAAATCAACCCAGATTTGGTCAGGGAGTTTCCAGATGT
CTTGGAATGCACTGTATCTCATGCAGTAAAAAAGATAAATCCTGAAGAAAGAGAAGAAATGAAAGTTTTTACAAAACTGT
TCATTGTGGGATCAAACTCTTCATCATCAACTAGAAATGTGCTTGGCATAGCCTGTCAAGTCCTTGGAGTTCCACAGCTG
GACTCTGTGATCATTGCATCACCTCCCATTGAAGAGGGGGTTAATCTATCCTTGGAGTACTTACAACCTTACTGGAAGGA
ATTAGAAAACTTAGTTCAGAGCAAAAAGATTGTTGATATAGGTACCACTGATCTGGACAAAACACAGCTGGAACAGCTGT
ATCAGTGGGCACAGGTTAAACCAAATAGTAACCAAGTTAATCTGGCCTCCTGCTGTGTGATGCCACCTGATTTGACTACA
TTTGTAAACAATTTGACATACAGTTCTTGACTCATAATGATCCACAA

Alignment

ORF - retro_tbel_3522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRDCIQKTLNEWSSQINPDLVREFPDVLECTVSHAVEKINPEEREEMKVSAKLFIVGSNSSSSTRNAVDM
          LR.CIQKTLN.WSSQINPDLVREFPDVLECTVSHAV.KINPEEREEMKV..KLFIVGSNSSSSTRN....
Retrocopy LRYCIQKTLNKWSSQINPDLVREFPDVLECTVSHAVKKINPEEREEMKVFTKLFIVGSNSSSSTRNVLGI

Parental  ACSVLGVAQLDSVIIASPPIED-VNLSLQHLQSYWEE-ENLVQSKRCAIV--SDLDXXXXXXXXXXXXVK
          AC.VLGV.QLDSVIIASPPIE..VNLSL..LQ.YW.E.ENLVQSK........DLD............VK
Retrocopy ACQVLGVPQLDSVIIASPPIEEGVNLSLEYLQPYWKELENLVQSKKIVDIGTTDLDKTQLEQLYQWAQVK

Parental  PNSNQVNLASCCVMPPDLTAF-AKQFDIQLLTHNDPK
          PNSNQVNLASCCVMPPDLT.F..KQFDIQ.LTHNDP.
Retrocopy PNSNQVNLASCCVMPPDLTTF<CKQFDIQFLTHNDPQ

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_3522 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3522 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012122	2 retrocopies	retro_chof_1710, retro_chof_765,
Tupaia belangeri	ENSTBEG00000006631	1 retrocopy	retro_tbel_3522 ,