RetrogeneDB ID: retro_tbel_3448

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_141059:91254..91730(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBDC1
• Ensembl ID: ENSTBEG00000003411
• Aliases: None
• Description: polysaccharide biosynthesis domain containing 1 [Source:HGNC Symbol;Acc:28790]

Sequence

>retro_tbel_3448
GCTACTAGTGGAACTGAGGAGCCATTTTCCAGGTAGCTGGTGTCTGTGGTGTCTGCTGTCCCAGCAGCATCATGGGCAGC
TTTCCTGACATTGAGGTGGCTTGGGCCATGAGAGCAGTGCATGCTGAAGTCCATTACGAGCTGATTCCATCAGTTGACTC
TCAGTTCCTGAAACTCACCAAAGTGCAGGACTAAATCTACTCTGAATTATAGGAAGTCTTTGAGAAATTCAGGATAAACG
TATCGGACCCAGAAGAACTCAAGTCAGAATCAGCTAAAGAGAAGTGGACGGCATTTTGCGTGAAGTTGGATAGGACTGTA
GAAGACTGCAACTGTGGTGCTTTATTACGACTAGATTGTTCTCAGGGTTACACTGAGGAAAATACCATTTTTGTCCTCAG
GATTCAAGTTTTTGCCATTGAAATTGCTTGAAACCAGGAAGGCTATAACAAAGCAGTTTCTATCAGTGTTCAGGAC

Alignment

ORF - retro_tbel_3448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.26 %
• Parental protein coverage: 72.35 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASSGTDE-VSGELLSVAHALSLPAESY-GNDPDIEMAWAMRAMQHAEVYYKLISSVDPQFLKLTKVDDQI
          A.SGT.E..S..L.SV..A...PA.S..G..PDIE.AWAMRA..HAEV.Y.LI.SVD.QFLKLTKV.D.I
Retrocopy ATSGTEEPFSR*LVSVVSAV--PAASW<GSFPDIEVAWAMRAV-HAEVHYELIPSVDSQFLKLTKVQD*I

Parental  YSEFREIFEKLRIDVLDPEELKSESAKEKWRPFCMKFDGIVEDFNYGTLLRLDSQ--YTEET--IAPRIQ
          YSE..E.FEK.RI.V.DPEELKSESAKEKW..FC.K.D..VED.N.G.LLRLD....YTEE......RIQ
Retrocopy YSEL*EVFEKFRINVSDPEELKSESAKEKWTAFCVKLDRTVEDCNCGALLRLDCSQGYTEENTIFVLRIQ

Parental  FFAIEIARNREGYNKAVYISVQD
          .FAIEIA.N.EGYNKAV.ISVQD
Retrocopy VFAIEIA*NQEGYNKAVSISVQD

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_3448 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3448 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017228	2 retrocopies	retro_cfam_1588, retro_cfam_944,
Callithrix jacchus	ENSCJAG00000018571	1 retrocopy	retro_cjac_1880,
Equus caballus	ENSECAG00000009882	1 retrocopy	retro_ecab_532,
Erinaceus europaeus	ENSEEUG00000001116	1 retrocopy	retro_eeur_377,
Monodelphis domestica	ENSMODG00000009685	2 retrocopies	retro_mdom_1002, retro_mdom_572,
Mus musculus	ENSMUSG00000031226	1 retrocopy	retro_mmus_1569,
Oryctolagus cuniculus	ENSOCUG00000001088	3 retrocopies	retro_ocun_1017, retro_ocun_1402, retro_ocun_595,
Otolemur garnettii	ENSOGAG00000015205	1 retrocopy	retro_ogar_3063,
Rattus norvegicus	ENSRNOG00000002662	3 retrocopies	retro_rnor_1703, retro_rnor_1705, retro_rnor_826,
Sarcophilus harrisii	ENSSHAG00000017872	1 retrocopy	retro_shar_132,
Tupaia belangeri	ENSTBEG00000003411	3 retrocopies	retro_tbel_3448 , retro_tbel_494, retro_tbel_979,