RetrogeneDB ID: retro_etel_1888

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_311874:44342..44552(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC2L
• Ensembl ID: ENSETEG00000003547
• Aliases: None
• Description: trafficking protein particle complex 2-like [Source:HGNC Symbol;Acc:30887]

Sequence

>retro_etel_1888
TACGGCTACGTGACCAACTCCAAGGTGGAGTTTGTGATGGTGGTGGACTTATCGAACAAGGCGCTGAGAGTCAACGAGAT
CTGCAGCATGTTCCGGAAGCTGCATAATTCCTACACTGACGTCATGTGCAACCCCTTCTACAACCCCGGGGACTGCATTC
ACTCTAGGGCCTTCGACAGCACCGTGACGTCCATGATGACACATGTCTGC

Alignment

ORF - retro_etel_1888 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.73 %
• Parental protein coverage: 50.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YGYVTNSKVKFVMVVDSSNTALRDNEIRSMFRKLHNSYTDVMCNPFYNPGDRIHSSRAFDSTVTSMMTQV
          YGYVTNSKV.FVMVVD.SN.ALR.NEI.SMFRKLHNSYTDVMCNPFYNPGD.IH.SRAFDSTVTSMMT.V
Retrocopy YGYVTNSKVEFVMVVDLSNKALRVNEICSMFRKLHNSYTDVMCNPFYNPGDCIH-SRAFDSTVTSMMTHV

Parental  C
          C
Retrocopy C

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_1888 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000003547	1 retrocopy	retro_etel_1888 ,
Homo sapiens	ENSG00000167515	1 retrocopy	retro_hsap_4852,
Monodelphis domestica	ENSMODG00000003889	2 retrocopies	retro_mdom_1165, retro_mdom_1391,
Rattus norvegicus	ENSRNOG00000014581	3 retrocopies	retro_rnor_1444, retro_rnor_1866, retro_rnor_2239,