RetrogeneDB ID: retro_tbel_3453

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_14128:118806..119374(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000014175
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSTBEG00000010363
• Aliases: None
• Description: ribosomal protein L8 [Source:HGNC Symbol;Acc:10368]

Sequence

>retro_tbel_3453
CTCCGCGTGGTGGACTTCGCTGAGCAGCACGGCTACATCAAGGGCATCATAAAGGACATCATCAATGACCCGAGCAACAG
CTCGTCCCTCACCAAATGGCCTTCCGGGACCCGTACAGGTTTCAGAAGTGGACCGAGCTGTTCATCGCCACCGAGGGCAT
CCACAAGGACGGACCAGTTCGTGTACTGCGGCAAGAAGGCGCAGCTCAACAGGGGCAGTGTCCTACCCGTGGGCACCATC
CTGGAGGTACGATTGCTGCTTGGAAGAGAAGCCTGGGGACCGCGCAAGCCAGCCCAGGCCTCCGGAAACTATGTTACCGT
CATCTCCCACAACCCGGAGACCAAGACCCAAGTGAAGCTGCCCTCGGGCTCCACGAAGGTCATCTCCTCCGCCAACAGAG
CTGTGGTCGGTGTGCAGGCTGGAGGTGGGGGGATTGACAAACCTATCCCGAAGGTTGGCGGTGCCTATCTAAAATAAGAC
AGAGGAACTGTTGGCCCACGTGTGCGGGCTGTGGCTATGAGTCAGTGGGACTCCCTTTGGAGGTGGCGACCATCATTACA
TCCGCAAA

Alignment

ORF - retro_tbel_3453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.88 %
• Parental protein coverage: 88.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK-VVFRDPYRFKKRTELFIAAE-GIHTGQFVYCGKKAQL
          LR.VDFAE.HGYIKGI.KDII.DP.....L.K...FRDPYRF.K.TELFIA.E.G...G....C......
Retrocopy LRVVDFAEQHGYIKGIIKDIINDPSNSSSLTK<MAFRDPYRFQKWTELFIATE<GHPQGRTSSCTAARRR

Parental  NIGNVLPVGTMPEGTIVCCLEEKPGDRG-KLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAV
          ...........P.....CCLEEKPGDR..K.A.ASGNY.TVISHNPETK.T.VKLPSGS.KVISSANRAV
Retrocopy SSTGAVSYPWAPSWRYDCCLEEKPGDRA<KPAQASGNYVTVISHNPETK-TQVKLPSGSTKVISSANRAV

Parental  VGVVAGGGRIDKPILTAGRGQKYKVNRNCWPRVPLVAM-KSVEHP-FGGGDHQHISK
          VGV.AGGG.IDKPI...G............PRV..VAM..SV..P.FGGGDH..I.K
Retrocopy VGVQAGGGGIDKPIPKVGGAYLK*DRGTVGPRVRAVAM<ESVGLP<FGGGDHHYIRK

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_3453 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3453 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Canis familiaris	ENSCAFG00000001677	1 retrocopy	retro_cfam_1132,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,
Tupaia belangeri	ENSTBEG00000010363	2 retrocopies	retro_tbel_2826, retro_tbel_3453 ,