RetrogeneDB ID: retro_etel_1223

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_231063:2546..3218(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000013403
• 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_1223
GGTAAACTCAACATCCACAGCATCATCCAATGGCTGCTGCAAGTGAGAGCATCCAAGCCTGGGAGGAATGTCCAACTCCA
GGAGAATGAAATCAGGGGTCTGTGCTCAAAGTCTCGGGAGAACTTTCTCAGGCAGCCTATCCTGCTAGAACTTGAAGCGC
CACTCAAAATAGGTGGTGACATCTATGGGCAATACTATGCTTTGCTTCGACTCTTCGAGTACGGAGGTTTCCCACCAGAA
AGCAACTACCCATTTCTTGGGGGCTACGTAGACCGGGGAAAGCAGTCCTCAGAGACGATCTGCCTCTTAGTGGCCTACAA
AATAAAATACCCCAAGAACTTTTTTCTTCTCAGAGGGAACCATGATTGTGCCAGCATCAATAGAATTTATGGATTTTATG
ATGAATGTAAAAGAAGATGCAATATTAAACTCTGGAAAACGTTTACAGACTGCTTTAACTGCTTGCCAATAGCCACCATC
ATGGATGAGAAAATATTCTGCTGTCATGGAGGTTTATCACCAGATCTTCAATCTATGGAGCATATTCGGTGAATTATGCG
ACCAACTGATGTACCTGATCAAGGTCTCCTTTGTGATCTTTTGTGGTCTGACCTCGATAAAGATGTCTTAGGCTGGGGTG
AAAATGACAGAGGAGTCTCCTTCACATTTGGT

Alignment

ORF - retro_etel_1223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.59 %
• Parental protein coverage: 68.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GELNVDSLITRLLEVRGCRPGKIVQMTEAEVRGLCIKSREIFLSQPILLELEAPLKICGDIHGQYTDLLR
          G.LN..S.I..LL.VR...PG..VQ..E.E.RGLC.KSRE.FL.QPILLELEAPLKI.GDI.GQY..LLR
Retrocopy GKLNIHSIIQWLLQVRASKPGRNVQLQENEIRGLCSKSRENFLRQPILLELEAPLKIGGDIYGQYYALLR

Parental  LFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFCDECKRRF
          LFEYGGFPPE.NY.FLG.YVDRGKQS.ETICLL.AYKIKYP.NFFLLRGNH.CASINRIYGF.DECKRR.
Retrocopy LFEYGGFPPESNYPFLGGYVDRGKQSSETICLLVAYKIKYPKNFFLLRGNHDCASINRIYGFYDECKRRC

Parental  NIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGLLCDLLWSDPDKDVQ
          NIKLWKTFTDCFNCLPIA.I.DEKIFCCHGGLSPDLQSME.IR.IMRPTDVPD.GLLCDLLWSD.DKDV.
Retrocopy NIKLWKTFTDCFNCLPIATIMDEKIFCCHGGLSPDLQSMEHIR*IMRPTDVPDQGLLCDLLWSDLDKDVL

Parental  GWGENDRGVSFTFG
          GWGENDRGVSFTFG
Retrocopy GWGENDRGVSFTFG

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_1223 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,