RetrogeneDB ID: retro_tbel_2300

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_108750:102135..102790(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPRG1L
• Ensembl ID: ENSTBEG00000011399
• Aliases: None
• Description: tumor protein p63 regulated 1-like [Source:HGNC Symbol;Acc:27007]

Sequence

>retro_tbel_2300
ATACTGCAGCTGCGGGACTCTGTAGACTTGGCGGGCACTAGCCCCATGGCACTGCTGGTGGCCGACGAGGAGGAGGCCGC
AGGTGGCGGCCTGGGCGGAGGACGACCTGGGGCCAGCATGCCGCTGCTCCAGACACTGTGGCCGCTCAGCGTACACGACC
CACCCGCCGCGCCCGTGTCAAGGAGTACTTCGTGTTCCGACCTGGCACCATCAAGCAGGCAGTGGAGGAGATCCGTGTGG
TGGTCTGACCAGTGGAGGATGGCGAGATCCGGGGGGTGTGGCTGCTGACCGAGGTGGACCACTGGAACAACGAGAAGGAA
CAGCTGGTGCTGATCACTGACCAGTCATTGCTTATCTGCAAATATGACTTCATTAATCTTCAGTGCCCACAGGTGGTCAG
GATTGCACTCAATGCAGTGGATACCATCTCATAGGAGAATTTCAGTTTCCCCCTAAATCACTCAACAAGTGAGAAGGCTT
TGGGATTCTCAACAGGGACAAGCAAAGTCGCCCTTCCTTCATCAACAGATGGAATCCCTGGTCTACAAATGTGCCCTATG
CCACGTTCATAGAACACCCAATGGCCGGTGCAGATGAGAAGACGGCCTCTCTGTGCCAAGTAAGACAGCCACACTGCTTG
GCAGTGACAGAAGTG

Alignment

ORF - retro_tbel_2300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.14 %
• Parental protein coverage: 80.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLQLRDSVDSAGTSPTALLAADEEEASGGGLGGVRPGAGT-LRQTLWPLSVHDP-TRRARVKEYFVFRPG
          .LQLRDSVD.AGTSP.ALL.ADEEEA.GGGLGG.RPGA...L.QTLWPLSVHDP.TRRARVKEYFVFRPG
Retrocopy ILQLRDSVDLAGTSPMALLVADEEEAAGGGLGGGRPGASMPLLQTLWPLSVHDP<TRRARVKEYFVFRPG

Parental  TIEQAVEEIRVVVRPVEDGEIQGVWLLTEVDHWNNEKERLVLITDQSLLICKYDFINLQCQQVVRIALNA
          TI.QAVEEIRVVV.PVEDGEI.GVWLLTEVDHWNNEKE.LVLITDQSLLICKYDFINLQC.QVVRIALNA
Retrocopy TIKQAVEEIRVVV*PVEDGEIRGVWLLTEVDHWNNEKEQLVLITDQSLLICKYDFINLQCPQVVRIALNA

Parental  VDTIS-YGEFQFPPKSLNKREGFGIRIQWDKQSRPSFINRWNPWSTNVPYATFIEHPMAGADEKTASLCQ
          VDTIS..GEFQFPPKSLNK.EGFGI....DKQSRPSFINRWNPWSTNVPYATFIEHPMAGADEKTASLCQ
Retrocopy VDTIS<IGEFQFPPKSLNK*EGFGI-LNRDKQSRPSFINRWNPWSTNVPYATFIEHPMAGADEKTASLCQ

Parental  LESFKALLIQAV
          ......L....V
Retrocopy VRQPHCLAVTEV

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_2300 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2300 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006651	1 retrocopy	retro_mdom_1017,
Pteropus vampyrus	ENSPVAG00000015273	1 retrocopy	retro_pvam_1018,
Ictidomys tridecemlineatus	ENSSTOG00000007466	1 retrocopy	retro_itri_28,
Tupaia belangeri	ENSTBEG00000011399	7 retrocopies	retro_tbel_1982, retro_tbel_2169, retro_tbel_2300 , retro_tbel_2302, retro_tbel_2339, retro_tbel_2599, retro_tbel_2603,