RetrogeneDB ID: retro_etel_615

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_102981:907..1527(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000010238
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SIKE1
• Ensembl ID: ENSETEG00000007805
• Aliases: None
• Description: suppressor of IKBKE 1 [Source:HGNC Symbol;Acc:26119]

Sequence

>retro_etel_615
ATGACCTGCACCATCGAAAAGATCCTGACAGATGCCAAGACGCTGCTGACGAGGCTACGGGAACACGATGCAGCCGCTGA
GTCGCTAGTGGATCAGTCAACGGCCAGCACCAGTGGGTGGCAGCTATGCGGGAGGCCGGGGCAGCGCTTCTGGACCAGTA
TCAAGAGGATGCACCCGATATGAAGGACATGACCAAATACAAGCCTCACGTTCTCCTGTCCCAAGAGAACACACAGATTA
GGGATTTGGAGCAAGAAAACAGAGAGCTGTGGGTTTCCCTGGAGGAACACCAGGGTGCCTTGGAGCTGATCCTGAGCAAG
TACCAGAAACCGATGTTGGAATTGGTGGTTGCTAAGGAAGCAGTCGATGCTGAACCAGTCCTGAAAGCTCACCAGTCTCA
TTCTGCAGAAATTGAAAGTCAAATGGACAGAATCTGTGAAATGGGAGAAGTCATGAGGAAAGCCGTTCAGGTGGATGATG
ATCAGTTCTGTGAGGTTCAGGAGAAGCTAGCCCAGTCAGAGCTTGAAAATAAGGAACTTCGAGGAGTATTGTCTCTCATC
AGTGAGTCACTTCGAGTCAGGAGGGAAGACTCAATGGACACTGCTTTCCAAGCCATCAAA

Alignment

ORF - retro_etel_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.43 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTCTIEKILTDAKTLLERLREHDAAAESLVDQSAAL-HRRVAAMREAGAALPDQVRPGYPEDAPDAKDMT
          MTCTIEKILTDAKTLL.RLREHDAAAESLVDQS.A..H..VAAMREAGAAL.DQ....Y.EDAPD.KDMT
Retrocopy MTCTIEKILTDAKTLLTRLREHDAAAESLVDQSTAS<HQWVAAMREAGAALLDQ----YQEDAPDMKDMT

Parental  KYKPHILLSQENTQIRDLQQENRELWVSLEEHQDALELIMSKYRKQMLQLMVAKKAADAEPVLRAHQSHS
          KYKPH.LLSQENTQIRDL.QENRELWVSLEEHQ.ALELI.SKY.K.ML.L.VAK.A.DAEPVL.AHQSHS
Retrocopy KYKPHVLLSQENTQIRDLEQENRELWVSLEEHQGALELILSKYQKPMLELVVAKEAVDAEPVLKAHQSHS

Parental  AEIESQIDRICEMGEVMRKAVQVDDDQFCKVQEKLAQLELENKELRELLSISSESLQVRRKDSMDTAFQA
          AEIESQ.DRICEMGEVMRKAVQVDDDQFC.VQEKLAQ.ELENKELR..LS..SESL.VRR.DSMDTAFQA
Retrocopy AEIESQMDRICEMGEVMRKAVQVDDDQFCEVQEKLAQSELENKELRGVLSLISESLRVRREDSMDTAFQA

Parental  IK
          IK
Retrocopy IK

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_615 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012958	1 retrocopy	retro_chof_48,
Echinops telfairi	ENSETEG00000007805	1 retrocopy	retro_etel_615 ,
Loxodonta africana	ENSLAFG00000010502	1 retrocopy	retro_lafr_565,
Microcebus murinus	ENSMICG00000015446	1 retrocopy	retro_mmur_738,
Otolemur garnettii	ENSOGAG00000005952	2 retrocopies	retro_ogar_1794, retro_ogar_2028,
Ictidomys tridecemlineatus	ENSSTOG00000001684	1 retrocopy	retro_itri_1447,
Tupaia belangeri	ENSTBEG00000007772	1 retrocopy	retro_tbel_2455,