RetrogeneDB ID: retro_etel_417

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_6993:75424..75868(-)
• Located in intron of: ENSETEG00000016613

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSRP1
• Ensembl ID: ENSETEG00000017067
• Aliases: None
• Description: cysteine and glycine-rich protein 1 [Source:HGNC Symbol;Acc:2469]

Sequence

>retro_etel_417
CCGAACTGGGGAGGAGGCAAGAAGTGTGGGGTGTGCCAGAAGACGGTCTACTTTGCCGAAGAGGTTCAGTGCGAAGGCAG
TAGCTTCCATAAATCCTGCTTCCTGTGCATGGTCTGCAAGAAAAACCTGGACAGTACCACCGTGGCTGTGCACGGCAAGT
CCTGCTACGGCAAGAAGTATGGGCCCAAAGGCTACGGCTACGGCCAGGGCGCAGGCACGCTGAGCACTGACAAGGAGTCG
CTGGGCATTAAGCATGAGGAGGCCCCTGGCCACAGGCCCACCAGCAACCCCAACGCGTCCAAGTTTCCCCAGAAAATTGG
TGGTTCGGAGTGCTGTCCCCGCTGCAGTCAGGCTGTCTGTGCTGCGGAGGTGATTGGCACCGGGAAGTCCTGGCACAAGT
CCTGTTTCCGGAGTGGCAAGAGCCTTGAGTTAACCACTCTGGCG

Alignment

ORF - retro_etel_417 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.28 %
• Parental protein coverage: 81.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PNWGGGKKCGVCQKTVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKACYGKKYGPKGY
          PNWGGGKKCGVCQKTVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHG...Y.K..YG....PKGY
Retrocopy PNWGGGKKCGVCQKTVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGKSCYGKK-YG----PKGY

Parental  GYGQGAGTLSTDKGESLGIKHEEAPGHRPTSNPNASKFAQKIGGSERSCC---SQAVYAAEVIGAGKSWH
          GYGQGAGTLSTDK.ESLGIKHEEAPGHRPTSNPNASKF.QKIGGSE..CC...SQAV.AAEVIG.GKSWH
Retrocopy GYGQGAGTLSTDK-ESLGIKHEEAPGHRPTSNPNASKFPQKIGGSE--CCPRCSQAVCAAEVIGTGKSWH

Parental  KSCFRCAKCGKGLESTTLA
          KSCFR....GK.LE.TTLA
Retrocopy KSCFR---SGKSLELTTLA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_417 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012114	1 retrocopy	retro_amel_1294,
Echinops telfairi	ENSETEG00000017067	1 retrocopy	retro_etel_417 ,
Echinops telfairi	ENSETEG00000019648	1 retrocopy	retro_etel_1589,
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,
Drosophila melanogaster	FBgn0259209	1 retrocopy	retro_dmel_71,