RetrogeneDB ID: retro_etel_1883

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_311449:58476..58788(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBPL1
• Ensembl ID: ENSETEG00000015892
• Aliases: None
• Description: TBP-like 1 [Source:HGNC Symbol;Acc:11589]

Sequence

>retro_etel_1883
AGCAGGGGGTTAGCTCACAGTCTGCAGAAACTGGGTTCTGGGGTAATATCTACAGATTTTAAGGTGCTGATGTTTGGGCA
CTGTGGAACATGCCACTGGAAATCCGTTAGCCAGAATTCACCAAGAACAATAAACCCCATGTCGGTGAGAAGACCAGACG
TCATCCTGCAGGGGTTTCTGGAATAAAAGCCCTCCGAGCTACAGGACGGATGTTCTCCAACAGCAAATATCCCAGTCACG
GGGCCTGGTGGCAACGCTGTAGCTGGTGCGGAGGAACAGATCGGCCCATTGGGTTTGAAAGCAGCCAAGGAA

Alignment

ORF - retro_etel_1883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.66 %
• Parental protein coverage: 93.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARRLARSLQKLF--VIFTDFKVV-NVLAVCNMPFEIRLPEFTKNNRPHASYEPELHPAVCYRIKSLRATL
          .R.LA.SLQKL...VI.TDFKV...V.A..NMP.EIR.PEFTKNN.PH.......HPA....IK.LRAT.
Retrocopy SRGLAHSLQKLGSGVISTDFKVL<DVWALWNMPLEIR*PEFTKNNKPHVGEKTRRHPAGVSGIKALRATG

Parental  QIFS-TGSITVTGPNVKAVAAAVEQIYPFVFESRKE
          ..FS.T..I.VTGP...AVA.A.EQI.P......KE
Retrocopy RMFS>TANIPVTGPGGNAVAGAEEQIGPLGLKAAKE

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_1883 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007544	1 retrocopy	retro_chof_469,
Cavia porcellus	ENSCPOG00000011899	1 retrocopy	retro_cpor_575,
Echinops telfairi	ENSETEG00000015892	1 retrocopy	retro_etel_1883 ,
Monodelphis domestica	ENSMODG00000017515	1 retrocopy	retro_mdom_1220,
Otolemur garnettii	ENSOGAG00000006622	2 retrocopies	retro_ogar_1508, retro_ogar_1509,