RetrogeneDB ID: retro_etel_2021

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_3306:1910..2603(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNY
• Ensembl ID: ENSETEG00000005121
• Aliases: None
• Description: cyclin Y [Source:HGNC Symbol;Acc:23354]

Sequence

>retro_etel_2021
TTGAACATGGAATTCAATCCTTCAGATCATCCTCAGGCCAGCACAACATTCCTCAGTAAATCTCGGACGGATGTGAGAGA
AAAACGCAAGAGTCTCTTCATTAACTATCATCCTCCAGGACAAATAGCACGGAATTACAGCTCCTGCTCCACTATCTACC
TAGACGATAGTACAGTCAGTCAACGAAACCTCAAGTATACAATTAAATGTGTAGCTCTCGCAATATATTATCACATCAAA
AACAGGGACCCAGATGGAAGGATGCTCTTAGATATTTTTTATGAAAACCTTCACCCTCTCTCGAAATCCGAAGTGCCACC
TGACTATGACAAACACAACCCAGAGCAGAAACAGATTTACCAGTTTGTTCGGCCACTGTTCAGTGCTGCCCAGCTGATGG
CAGAATGTGCCACTGTCACCCTGGTTTACCTCGAACGAATTCTGAGGTACGTGGAGATAGACATCTGCCTGGCCAACTGG
AAGCGCATTGTCCTGGGTGCCATCCTGCTGGCCTCCAAGGTGTGGGACGACCAGGCGGTCTAGAAGGTGGACTACAGCCA
GATCCTGAAGGACATCATGGTGGCGCACATGAACGAGCTCGAAAGGCAGTTTCTTGAATTGCTCCAGTTCAACATCAACG
TTCCCTCCAGTGTTTACCCCAAGTATTATTTTGACCTCCGTTTGACAGCTGAG

Alignment

ORF - retro_etel_2021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.18 %
• Parental protein coverage: 79.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LNMEFNPSDHPRASTIFLSKSQTDVREKRKSLFINHHPPGQIARKYSSCSTIFLDDSTVSQPNLKYTIKC
          LNMEFNPSDHP.AST.FLSKS.TDVREKRKSLFIN.HPPGQIAR.YSSCSTI.LDDSTVSQ.NLKYTIKC
Retrocopy LNMEFNPSDHPQASTTFLSKSRTDVREKRKSLFINYHPPGQIARNYSSCSTIYLDDSTVSQRNLKYTIKC

Parental  VALAIYYHIKNRDPDGRMLLDIFDENLHPLSKSEVPPDYDKHNPEQKQIYRFVRTLFSAAQLTAECAIVT
          VALAIYYHIKNRDPDGRMLLDIF.ENLHPLSKSEVPPDYDKHNPEQKQIY.FVR.LFSAAQL.AECA.VT
Retrocopy VALAIYYHIKNRDPDGRMLLDIFYENLHPLSKSEVPPDYDKHNPEQKQIYQFVRPLFSAAQLMAECATVT

Parental  LVYLERLLTYAEIDICPANWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNELERQFLELLQF
          LVYLER.L.Y.EIDIC.ANWKRIVLGAILLASKVWDDQAV..VDY.QILKDI.V..MNELERQFLELLQF
Retrocopy LVYLERILRYVEIDICLANWKRIVLGAILLASKVWDDQAV*KVDYSQILKDIMVAHMNELERQFLELLQF

Parental  NINVPSSVYAKYYFDLRSLAE
          NINVPSSVY.KYYFDLR..AE
Retrocopy NINVPSSVYPKYYFDLRLTAE

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_2021 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006201	1 retrocopy	retro_chof_2504,
Echinops telfairi	ENSETEG00000005121	1 retrocopy	retro_etel_2021 ,
Loxodonta africana	ENSLAFG00000012820	1 retrocopy	retro_lafr_79,
Pan troglodytes	ENSPTRG00000002421	2 retrocopies	retro_ptro_1322, retro_ptro_3228,