RetrogeneDB ID: retro_tbel_3783

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_15317:51562..52473(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERGIC2
• Ensembl ID: ENSTBEG00000011223
• Aliases: None
• Description: ERGIC and golgi 2 [Source:HGNC Symbol;Acc:30208]

Sequence

>retro_tbel_3783
GAATTGAGAATCAATATAGAGATTACTGTTGCCATGAAATGTCAATATGTTGGAGCAGATGTACTGGATTTAGCAGAAAC
AATGGTTGCATCTGCAGATGGTCTAGTTTATGAACCAGAAATATTTGATCTTTCACCACAGCAAAAAGAGTGGCAAAGGA
TACTTCAAGTGATTCAGAGTAGGCTGCAAGAAGAGCAATCACTTCAAGATGTGATATTTAAAAGTGCTTTTAAAGGTACA
GCCGCACTTCCCCCCAAGAGAAGATGGTTCATTACGGCCTCCAGATGCAGGCAGAATTCATGGTCATCTGTATGTCAATA
AAGTAGCAGGGAATTTTCGCATTACTGTGGGCAAGGCAACTCCACATCGTTGTGGTCACACATACCTGGCAACACTCGTC
AAACATGACTCTTACAACTTTTCCCACAGAATGGATCATTTGTCTTTTTGCAAGCTTTTCCAGGAATTATTAAACCTTTA
CTTGGAACTGAAAAAATTGCTGTAGATCACAACCAGATGTTCCAATATTTTATTACAGTTGTGCCAACAAAACTACATAC
ATATAAAATTTCAGCAGACAACTATCAGTTTCTGTGACAGAACGGGAACGTATTATTAACCATGCTGCAGGCAGCTACAG
AGTATCTGGGATATTTATGAAATATGATCTCAGTTCTCTTATGGTGACAGTTACTGAGGAGCACATGCCATTCTGGCAGT
TTTTTGTAAGACTCTGTGGTATTGTTGGAGGAATCTTTTCAACAACAGGCATGTTACATAGAATTGGAAAATTTATAGTC
GAAATAATTTGCTGCTGTTTCAGACTCGGATCCTACAAGCCTATCAATTCTGTCTCCTTTGAGGATGTCCACACAGACAT
CCACTTACCTCTTTTAGAAAATAATACACAT

Alignment

ORF - retro_tbel_3783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.67 %
• Parental protein coverage: 79.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLRINIDITVAMKCQYVGADVLDLAETMVASADGLVYEPAIFDLSPQQKEWQRMLQVIQSRLQEEHSLQD
          .LRINI.ITVAMKCQYVGADVLDLAETMVASADGLVYEP.IFDLSPQQKEWQR.LQVIQSRLQEE.SLQD
Retrocopy ELRINIEITVAMKCQYVGADVLDLAETMVASADGLVYEPEIFDLSPQQKEWQRILQVIQSRLQEEQSLQD

Parental  VIFKSAFKGTTALPP-REDGSLQPPDACRIHGHLYVNKVAGNFHITVGKAIPHPRGHAHLAALVNHDSYN
          VIFKSAFKGT.ALPP.REDGSL.PPDA.RIHGHLYVNKVAGNF.ITVGKA.PH..GH..LA.LV.HDSYN
Retrocopy VIFKSAFKGTAALPP>REDGSLRPPDAGRIHGHLYVNKVAGNFRITVGKATPHRCGHTYLATLVKHDSYN

Parental  FSHRIDHLSFGELV-PGIINPLDGTEKIAVDHNQMFQYFITVVPTKLHTYKISADTHQF-SVTERERIIN
          FSHR.DHLSF..L..PGII.PL.GTEKIAVDHNQMFQYFITVVPTKLHTYKISAD..QF.SVTERERIIN
Retrocopy FSHRMDHLSFCKLF<PGIIKPLLGTEKIAVDHNQMFQYFITVVPTKLHTYKISADNYQF<SVTERERIIN

Parental  HAAGSHGVSGIFMKYDLSSLMVTVTEEHMPFWQFFVRLCGIVGGIFSTTXXXXXXXXXXXXIICCCFRLG
          HAAGS..VSGIFMKYDLSSLMVTVTEEHMPFWQFFVRLCGIVGGIFSTT............IICCCFRLG
Retrocopy HAAGSYRVSGIFMKYDLSSLMVTVTEEHMPFWQFFVRLCGIVGGIFSTTGMLHRIGKFIVEIICCCFRLG

Parental  SYKPVNSVFFEDVHTDNHLPLLENNTH
          SYKP.NSV.FEDVHTD.HLPLLENNTH
Retrocopy SYKPINSVSFEDVHTDIHLPLLENNTH

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_3783 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3783 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015668	1 retrocopy	retro_cpor_824,
Ornithorhynchus anatinus	ENSOANG00000010582	1 retrocopy	retro_oana_32,
Oryctolagus cuniculus	ENSOCUG00000017255	1 retrocopy	retro_ocun_1540,
Pongo abelii	ENSPPYG00000004390	1 retrocopy	retro_pabe_657,
Rattus norvegicus	ENSRNOG00000001852	1 retrocopy	retro_rnor_1557,
Sarcophilus harrisii	ENSSHAG00000004822	1 retrocopy	retro_shar_386,
Tupaia belangeri	ENSTBEG00000011223	1 retrocopy	retro_tbel_3783 ,