RetrogeneDB ID: retro_tbel_1750

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5627:130594..130948(-)
• Located in intron of: ENSTBEG00000017664

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGP
• Ensembl ID: ENSTBEG00000001803
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class P [Source:HGNC Symbol;Acc:3046]

Sequence

>retro_tbel_1750
TTGTCCAAAGCCACAGGGAAAATGGTGGAAAATTCACCGTCGCCATTGCCAGAAGGAGTGATTTATGGTTTTGTTCTTTT
CTTAAGTTCTCAATTTGGTTTCATACTTTATCTAGTGTGGGCATTTATTCCTGAATCTTGGCTAAACTCCTTAGGCTTAA
CATATTGGCCTCAAAAATACTGGGCGGTCGCATTACCAGTCTACCTCCTTATTACTATAGTGATCGGTTATGTACTCTTA
TTTGGAGTTAACATGATGAGTACCGCGCCACTCAACTCCATTCACACAATCACAGATAACTATGCTAAAAATCAGCAGCA
GAAGAAATACCAAGAAGAAGCCATTCCAGCATTA

Alignment

ORF - retro_tbel_1750 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.37 %
• Parental protein coverage: 88.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSKATGKMVENSPSPLPERAIYGFVLFLSSQFGFXXXXXXAFIPESWLNSLGLTYWPQKYWAVALPVYLL
          LSKATGKMVENSPSPLPE..IYGFVLFLSSQFGF......AFIPESWLNSLGLTYWPQKYWAVALPVYLL
Retrocopy LSKATGKMVENSPSPLPEGVIYGFVLFLSSQFGFILYLVWAFIPESWLNSLGLTYWPQKYWAVALPVYLL

Parental  ITVVIGYVLLFGVNMMSTAPLNSIHTITDNYAKNQQQKKYQEEAIPAL
          IT.VIGYVLLFGVNMMSTAPLNSIHTITDNYAKNQQQKKYQEEAIPAL
Retrocopy ITIVIGYVLLFGVNMMSTAPLNSIHTITDNYAKNQQQKKYQEEAIPAL

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_1750 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1750 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009702	4 retrocopies	retro_cfam_1022, retro_cfam_1559, retro_cfam_1976, retro_cfam_238,
Myotis lucifugus	ENSMLUG00000005475	3 retrocopies	retro_mluc_1419, retro_mluc_1444, retro_mluc_2084,
Monodelphis domestica	ENSMODG00000020988	1 retrocopy	retro_mdom_1807,
Mustela putorius furo	ENSMPUG00000008312	5 retrocopies	retro_mputfur_1069, retro_mputfur_1388, retro_mputfur_421, retro_mputfur_642, retro_mputfur_826,
Sarcophilus harrisii	ENSSHAG00000014284	1 retrocopy	retro_shar_548,
Tupaia belangeri	ENSTBEG00000001803	4 retrocopies	retro_tbel_1750 , retro_tbel_2361, retro_tbel_3162, retro_tbel_655,
Tursiops truncatus	ENSTTRG00000007711	3 retrocopies	retro_ttru_1043, retro_ttru_677, retro_ttru_883,
Vicugna pacos	ENSVPAG00000009781	3 retrocopies	retro_vpac_166, retro_vpac_387, retro_vpac_639,