RetrogeneDB ID: retro_tbel_4216

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_72061:393..940(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WBSCR22
• Ensembl ID: ENSTBEG00000007038
• Aliases: None
• Description: Williams Beuren syndrome chromosome region 22 [Source:HGNC Symbol;Acc:16405]

Sequence

>retro_tbel_4216
GCAGTCTCAGACCGAAACACAGAGGGAGATCTGCTTCTGGGGACATGGGCCATGGCATCCCCTTCAAACCAGGCTCCTTC
GATGGTGGTATCAGCATTTCTGCTGTGCAGTGGCTCTGCCATGCTAACAAGAAATCTGACATCCCTGCCAAGCACATGTT
TTGCTTTTTTCTTCTTTATTCTGTTCTCACCCATGGAGGCAGAGCTGTCCTGCAGTTGTACCCTGAGAACTCAGAGCAGT
TGGAACTAATCACAACCAAGGCCACCGGGGATGGCTACACTGGCAGTATGGTGGAACACTAAGCTACAGTACCAACGCAA
AGAAGTTTTACCTGTCTGTTTGCCGGGCCTTCAACCTTTGTGCCAAAGAGGATGAATAAAAATCAGAAGGAGGTTGAGGC
CAGCTTTACCAATGAGAGGGTTCCTCATAGGACCGTGAGGGCGGGTTGGTGAGAAAGAGCCAAGAGCGGGTGCTGGGGAA
GGAGCGCTGCAGGCGACAGGGCAAAGAGGTCGGACTCAACACCCAGTACACTGGCGGCAAGTGCAGG

Alignment

ORF - retro_tbel_4216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 66.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AALDRDTEVDLLLG-DMGQGI-FKPG-FDGCISISAVQWLCNANKKSDVPAKRLYCFFSSLYSVLVRGGR
          A..DR.TE.DLLLG.DMG.GI.FKPG.FDG.ISISAVQWLC.ANKKSD.PAK...CFF..LYSVL..GGR
Retrocopy AVSDRNTEGDLLLG<DMGHGIPFKPGSFDGGISISAVQWLCHANKKSDIPAKHMFCFFL-LYSVLTHGGR

Parental  AVLQLYPENSEQLELITTQATKAGFTGGMVVDYPNSAKAKKFYLCLFAGPSTFVPKGLNENQDEVEARES
          AVLQLYPENSEQLELITT.AT..G.TG.M.V.............CLFAGPSTFVPK..N.NQ.EVEA...
Retrocopy AVLQLYPENSEQLELITTKATGDGYTGSM-VEH*ATVPTQRSFTCLFAGPSTFVPKRMNKNQKEVEA---

Parental  TFTNER-FLTG-LRRGLVRKSREWVLEKKERRRRQGKEVRPDTQYTGRKRR
          .FTNER.FL.G....GLVRKS.E.VL..KER.RRQGKEV...TQYTG.K.R
Retrocopy SFTNER>FLIG>REGGLVRKSQERVL-GKERCRRQGKEVGLNTQYTGGKCR

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_4216 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4216 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016799	1 retrocopy	retro_cjac_2908,
Echinops telfairi	ENSETEG00000008874	1 retrocopy	retro_etel_1185,
Oryctolagus cuniculus	ENSOCUG00000017297	1 retrocopy	retro_ocun_758,
Tupaia belangeri	ENSTBEG00000007038	1 retrocopy	retro_tbel_4216 ,