RetrogeneDB ID: retro_etel_1364

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_254438:4653..5232(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000017014
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP1CB
• Ensembl ID: ENSETEG00000015038
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9282]

Sequence

>retro_etel_1364
AAACTCAACATCAACAGCACCATCCAATGGCTGCTGGAAAGGAGACGGTTCAAGCCTGGGAAGAATGTTCAGCTCCAGGA
AAACAAAATCAGAGGCCTGTGCTTAAAGTCTGGAAAGACCTAACTCAGTCAGACTGTCCTACTAGAACTTGAAGGGCCAC
TCAAAATAGATGGTGACATCCATGGGCAATATGATAATTTCTTCGACTCTTTGAGTACAATTGCTTCCCACCCAGAATGC
AATTACTGTTTCCAAGGGACAACATAGATCAGGTATAGTAGTCCCTGGAGACTATCTGCCTCTTATAGGCCTACAAAATC
AAATACTCCAAGAACTTTCTTATTCTCAGAGGGAACCACAGATGTGCCAGCATTCATAGAATTTATGGATTTATGATGAA
TGTGAATAAATTATTTAACATTAAACCTGGATAATGTTCACAGACTGTTTCAGTGGTATGCTAATAGCTGCCATCAGGGA
TAAGACAATATTCTGCTGTCACAGAGGTTTATCACCAGGTCTTCAACCTATGGAGCAGATTTGGGAAGTTACATGACTAA
TGATGTACCAGATCAAGGT

Alignment

ORF - retro_etel_1364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.39 %
• Parental protein coverage: 59.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ELNVDSLITRLLEVRGCRPGKIVQMTEAEVRGLCIKSREIFLSQPILLELEAPLKICGDIHGQYTDL-LR
          .LN..S.I..LLE.R...PGK.VQ..E...RGLC.KS....LSQ..LLELE.PLKI.GDIHGQY....LR
Retrocopy KLNINSTIQWLLERRRFKPGKNVQLQENKIRGLCLKSGKT*LSQTVLLELEGPLKIDGDIHGQYDNF<LR

Parental  LFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFCDECKRRF
          LFEY..FPP....LF..D..D....SLETICLL.AYKIKY..NF..LRGNH.CASI.RIYGF.......F
Retrocopy LFEYNCFPPRMQLLFPRDNIDQV**SLETICLL*AYKIKYSKNFLILRGNHRCASIHRIYGFMMNVNKLF

Parental  NIK-LWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRI-MRPTDVPDTG
          NIK..W..FTDCF....IAAI.D..IFCCH.GLSP.LQ.MEQI........DVPD.G
Retrocopy NIK<TWIMFTDCFSGMLIAAIRDKTIFCCHRGLSPGLQPMEQIWEV<YMTNDVPDQG

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_1364 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000859	5 retrocopies	retro_chof_2023, retro_chof_2063, retro_chof_2076, retro_chof_2154, retro_chof_539,
Echinops telfairi	ENSETEG00000015038	2 retrocopies	retro_etel_1223, retro_etel_1364 ,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Rattus norvegicus	ENSRNOG00000004612	2 retrocopies	retro_rnor_1455, retro_rnor_2344,