RetrogeneDB ID: retro_tbel_2176

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_103670:1967..2264(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSRP1
• Ensembl ID: ENSTBEG00000008991
• Aliases: None
• Description: cysteine and glycine-rich protein 1 [Source:HGNC Symbol;Acc:2469]

Sequence

>retro_tbel_2176
GCTCAACCCCACAGGCCTACGACAAATCCAAACACTTCTAAGTTTGCACAGAAGTTCGGGGGTCCTGAGAAGGGTTCCAG
ATGTGGAGATTCCGTGTATGCTGCTGAAAAGGTCATTGGTGCTGGAAAGCCCTGGCACAAAAATTGCTTCCGATGTGCCA
AGTGTGGGAAGAGCCTTGAATCAACAACTCTGGCTGGGAAAGAAGGTGAAATCTATTGTAAAGGATGCTATGCAAAGAAC
TTTGAACCCAAAGGATTTGGCTATTGCCAAGGAGCAGGGGCCCGTGTTCACGCTCAG

Alignment

ORF - retro_tbel_2176 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APGHRPTTNPNASKFAQKIGGSERCPRCSQAVYAAEKVIGAGKSWHKSCFRCAKCGKGLESTTLADKDGE
          A..HRPTTNPN.SKFAQK.GG.E...RC...VYAAEKVIGAGK.WHK.CFRCAKCGK.LESTTLA.K.GE
Retrocopy AQPHRPTTNPNTSKFAQKFGGPEKGSRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLAGKEGE

Parental  IYCKGCYAKNFGPK-FGFGQGAGALVHSE
          IYCKGCYAKNF.PK.FG..QGAGA.VH..
Retrocopy IYCKGCYAKNFEPKGFGYCQGAGARVHAQ

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_2176 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2176 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012114	1 retrocopy	retro_amel_1294,
Echinops telfairi	ENSETEG00000017067	1 retrocopy	retro_etel_417,
Macaca mulatta	ENSMMUG00000020772	1 retrocopy	retro_mmul_1505,
Mus musculus	ENSMUSG00000026421	1 retrocopy	retro_mmus_2226,
Pan troglodytes	ENSPTRG00000001836	2 retrocopies	retro_ptro_1920, retro_ptro_1922,
Tupaia belangeri	ENSTBEG00000008991	1 retrocopy	retro_tbel_2176 ,
Tupaia belangeri	ENSTBEG00000009767	3 retrocopies	retro_tbel_1866, retro_tbel_4404, retro_tbel_4407,
Drosophila melanogaster	FBgn0259209	1 retrocopy	retro_dmel_71,