RetrogeneDB ID: retro_etel_1632

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_284160:52363..53450(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000000002
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PGM3
• Ensembl ID: ENSETEG00000015655
• Aliases: None
• Description: phosphoglucomutase 3 [Source:HGNC Symbol;Acc:8907]

Sequence

>retro_etel_1632
TCTGTAATACACGGTGTGACTGTGTTGGGAGGTCAATTCCATGATTATGGCTTGTTAACAACACCGCAGCTGTACTACAT
GGTGTACTGTCGAAATACCAACGACCAGTATGAGCAGCCAAATGTGGAAGGTTACTATCAGAAACACGCCAAGGCTTTTG
TGGAACTTAACAAACAGGCTTCCTACACAGGAGATGAACGAAGAACAATTGAAGGCTGACTGTGCTAATGGTATCCGGGC
CCTGAAGCTGAGAGAAATGGAACACTACTTCTCCCCCAAGGTGTCAGTTCTCCTGTTCAATGCTGGGACCAAAGGGAAAC
TCAATCACTTATGTGGGGCTGATTTTGTGAAAAGTCTTCAGAAACCTCCTGAGGGAATGGAAATGAAGCCCAATGAAAGA
TGCTGTTCCTTTGATAGCGATGCAGACAGAATTGTTTATTACTACCGAGATGCTGATGGCCACTTTCATCTCATAGATGG
AGACAAAATAGCAATGCTCACTACCAGTTTCCTCAAAGAGCTTCTATTGGAGACTGGAGAAGATTTGAAGGTTGGTGTTA
TACAAACTGTGTATGCAAATGGAAGCTCAACAAGATATCTTGAAGAAGTGATGAAGGTACCTGTCTATTGTACTAAAACT
GGTGTAAAACACTTGCACCACAAGGCTCAAGAGTTTGACATTAGAATTTATTTTGAAGCAAATGGCCATGGCACAGTATT
ATTTAGTAAAGTTGCTGAAATGAAGATAGGACAACTAGCACAGGAACTAGAAGGTAATAAAAGGAAAGCCGCTCAGATTC
TTGAAAACATTATTGACCTATTTAACCAGGCAATTGGTGATGCTATTTCTGACATGCTGGTGATTGAAGCAATTTTAGCT
TTAAAGGGCATGACTGTACAACAGTGGGATGCTCTCTATACAGATATTCCAAACAGACAACTCAAAGTTAAGGTTGCAGA
CAGGCAAGTTATCGGTACCCCCAATGCTGAAAGACAGGCACTTACACCCCCAGGACTGCAGGATGCAATCAATGGTCTGG
TGAAGAAGTACAGACTTTCCCGGGCTTTTGTCCGGCCCTCTGGAACA

Alignment

ORF - retro_etel_1632 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.71 %
• Parental protein coverage: 70.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVIHGVTVLGGQFHDYGLLTTPQLHYMVYCRNTNGQYGQATVEGYYQKHAKAFVGLTKQASYTGDGCRT-
          SVIHGVTVLGGQFHDYGLLTTPQL.YMVYCRNTN.QY.Q..VEGYYQKHAKAFV.L.KQASYTGD..RT.
Retrocopy SVIHGVTVLGGQFHDYGLLTTPQLYYMVYCRNTNDQYEQPNVEGYYQKHAKAFVELNKQASYTGDERRT>

Parental  LKVDCANGVGALKLREMEHYFSPELSVLLCNDGTKGKLNHLCGADFVKSHQQPPEXXXXXXXXRCCSFDG
          LK.DCANG..ALKLREMEHYFSP..SVLL.N.GTKGKLNHLCGADFVKS.Q.PPE........RCCSFD.
Retrocopy LKADCANGIRALKLREMEHYFSPKVSVLLFNAGTKGKLNHLCGADFVKSLQKPPEGMEMKPNERCCSFDS

Parental  DVDRIVYDYRDADGHFHLIDGDKIATLISSFLKELLLEIGEDLKVGVIQTAYANGSSTRYLEEVMKVPVY
          D.DRIVY.YRDADGHFHLIDGDKIA.L..SFLKELLLE.GEDLKVGVIQT.YANGSSTRYLEEVMKVPVY
Retrocopy DADRIVYYYRDADGHFHLIDGDKIAMLTTSFLKELLLETGEDLKVGVIQTVYANGSSTRYLEEVMKVPVY

Parental  CTKTGVKHLHHKAQEFDIGIYFEANGHGTVLFSKVAEMKIRQLAQELEGNKRKAAQILENIIDLFNQAIG
          CTKTGVKHLHHKAQEFDI.IYFEANGHGTVLFSKVAEMKI.QLAQELEGNKRKAAQILENIIDLFNQAIG
Retrocopy CTKTGVKHLHHKAQEFDIRIYFEANGHGTVLFSKVAEMKIGQLAQELEGNKRKAAQILENIIDLFNQAIG

Parental  DAISDMLVIEAILALKGMTVQQWDALYTDIPNRQLKVKVADRQVISTTDAERQALTPPGLQDAIDGLVKK
          DAISDMLVIEAILALKGMTVQQWDALYTDIPNRQLKVKVADRQVI.T..AERQALTPPGLQDAI.GLVKK
Retrocopy DAISDMLVIEAILALKGMTVQQWDALYTDIPNRQLKVKVADRQVIGTPNAERQALTPPGLQDAINGLVKK

Parental  YRLSRAFVRPSGT
          YRLSRAFVRPSGT
Retrocopy YRLSRAFVRPSGT

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_1632 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015655	1 retrocopy	retro_etel_1632 ,