RetrogeneDB ID: retro_tbel_3290

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_136229:8682..9371(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBK
• Ensembl ID: ENSTBEG00000002239
• Aliases: None
• Description: PDZ binding kinase [Source:HGNC Symbol;Acc:18282]

Sequence

>retro_tbel_3290
TTATGTTCGACTCCATGTATAAATATCCCCACCTCACCATTCATACAGAAACTTGGCTTTGGTACTAGAGTAAATGTTTA
CCTAAAAAAATGATCTCCAAGAGGGTTGTCTCTTTCTCCTTGGGCTGTGAAAAAGATTAATCGTATATGCGATGATCATT
ATCAAAGTATGTAGCAAAAGAGACTAGCCGATGAAGCTAAGATTTTAAAAAGACTTCATCATCCATACATTGCAGGGTAT
CATGTTTTCACTGAAGCCAGCGATGGTAGTCTATGTCTTGCTATGGAATATGGAGGCGAAAAGTCTCTCAATGACTTAAT
AGAAGAATGGAAGAAAGACAGCCGAGATCCTTTTTAGCTGCCATAATTTTAAAAGTTGCTTTGAACGTGGCAAGAGGGTT
AAAGTATCTGCACCAAGAAAAGAAGCTGCTTCATGGAGATATAAAGTCCTCAAATGTCATTAAAGGAGATTTTGAAACAA
TTCAAATTTGTGATGTAGGAGTCTCTTGGCCATTGGATGAAAATACGACTGTGACTGACCCCGAGGCCTGTTACATCGGC
CCTGAGCCGTGGAGGCCCAAGGAGGCTTTGGAAGAGAATGGTATTATTACCGACAAGGCAGCCATATTTGCTTTCGGACT
TACTCTGTGGGAAATGATGACTTTATCTAGTCTACACATGGATCCTCCA

Alignment

ORF - retro_tbel_3290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.03 %
• Parental protein coverage: 76.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LCSTPCVNIPASPFMQKLGFGTGVNVYLMKRSPRGLSHSPWAVKKINPICDDHYRSVYQKRLTDEAKILK
          LCSTPC.NIP.SPF.QKLGFGT.VNVYL.K.SPRGLS.SPWAVKKIN.ICDDHY.S..QKRL.DEAKILK
Retrocopy LCSTPCINIPTSPFIQKLGFGTRVNVYLKK*SPRGLSLSPWAVKKINRICDDHYQSM*QKRLADEAKILK

Parental  SLHHPNIVGYRAFTEASEGSLCLAMENGGEKALNDLIEERNKDSREP-FPAAIILKALW--ARG-RYLHQ
          .LHHP.I.GY..FTEAS.GSLCLAME.GGEK.LNDLIEE..KDSR.P.F.AAIILK.....ARG..YLHQ
Retrocopy RLHHPYIAGYHVFTEASDGSLCLAMEYGGEKSLNDLIEEWKKDSRDP<FLAAIILKVALNVARGLKYLHQ

Parental  EKKLLHGDIKSSNVVIKGDFETIKICDVGVSLPLDENMTVTDPEACYIGTEPWKPKEALEENGIITDKAD
          EKKLLHGDIKSSN.VIKGDFETI.ICDVGVS.PLDEN.TVTDPEACYIG.EPW.PKEALEENGIITDKA.
Retrocopy EKKLLHGDIKSSN-VIKGDFETIQICDVGVSWPLDENTTVTDPEACYIGPEPWRPKEALEENGIITDKAA

Parental  IFAFGLTLWEMMTLSIPHINLP
          IFAFGLTLWEMMTLS..H...P
Retrocopy IFAFGLTLWEMMTLSSLHMDPP

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_3290 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3290 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021069	1 retrocopy	retro_btau_150,
Canis familiaris	ENSCAFG00000008369	1 retrocopy	retro_cfam_1694,
Dipodomys ordii	ENSDORG00000014896	1 retrocopy	retro_dord_697,
Myotis lucifugus	ENSMLUG00000009596	1 retrocopy	retro_mluc_713,
Monodelphis domestica	ENSMODG00000015986	1 retrocopy	retro_mdom_245,
Mus musculus	ENSMUSG00000022033	1 retrocopy	retro_mmus_2452,
Otolemur garnettii	ENSOGAG00000009887	1 retrocopy	retro_ogar_3495,
Tupaia belangeri	ENSTBEG00000002239	1 retrocopy	retro_tbel_3290 ,