RetrogeneDB ID: retro_eeur_332

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_258706:4646..5228(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATF1
• Ensembl ID: ENSEEUG00000008000
• Aliases: None
• Description: activating transcription factor 1 [Source:HGNC Symbol;Acc:783]

Sequence

>retro_eeur_332
GTATCATCTTTATTAGAAAGTGAGGAGTCTCAGGACTCATCCAACAGTATAGGTTCCTCACAGAAAGTCCACAGGATCCT
CGCACAGCGCCAATCTTACAGAAAAATTTTGAAAGACCTATCTTCTGAAGATACACGAGGCAGAAAAGGAGACGGAGAAA
ACCCTGGAGTTTCTGCTGTCACCTCTATGTCTGTCCCAGCTCCCATCTATCAGACTAGCACTGGACAGTACATTGCCATC
ACCCCAAATGGAGCCTTACAGCTGGCCAGTCCAGGCACAGATGGAGTACAGGGACTTCAGGGCATTCACCATGACAAATT
CAGGCAGCACTCAGCAAGGAACATTTCTTCAGTATGCACAGACCTCTGATGGACAGCAGATACTAGTGACCCAGCAATCA
GGTGATCATACAGACTGCATCAGGAGATATGCAGAACTATCAGATCCATACCACACCCTCAGCTACTTTCACAGCAACAG
ACTGTGGTGGATGACATCTCCTGGTGACTTCTTACATCGCAGACCACTTAAGACAGATGACTCCTCATTTGAAAAAGAGA
AATCAGGTTGATGAAAAACAGA

Alignment

ORF - retro_eeur_332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.92 %
• Parental protein coverage: 80.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VSSLSESEESQDSSDSIGSSQKVHGILARRPSYRKILKDLSSEDTRGRKGDGENPGISAVTSMSVPTPIY
          VSSL.ESEESQDSS.SIGSSQKVH.ILA.R.SYRKILKDLSSEDTRGRKGDGENPG.SAVTSMSVP.PIY
Retrocopy VSSLLESEESQDSSNSIGSSQKVHRILAQRQSYRKILKDLSSEDTRGRKGDGENPGVSAVTSMSVPAPIY

Parental  QTSTGQYIAIAPNGALQLASPGTDGVQGLQ-ALTMTNSGSTQQGTTILQYAQTSDGQQILV-PSNQVVVQ
          QTSTGQYIAI.PNGALQLASPGTDGVQGLQ.A.TMTNSGSTQQG.T.LQYAQTSDGQQILV.PSNQV..Q
Retrocopy QTSTGQYIAITPNGALQLASPGTDGVQGLQ>AFTMTNSGSTQQG-TFLQYAQTSDGQQILV>PSNQVIIQ

Parental  TASGDMQTYQIRTTPSAT-SLPQTVV-MTSPVT-LTSQTTKTDD-PQL-KREIRLMKNR
          TASGDMQ.YQI.TTPSAT.S..QTVV.MTSP...L.....KTDD.P.L.KREIRLMKNR
Retrocopy TASGDMQNYQIHTTPSAT>SQQQTVV>MTSPGDFLHRRPLKTDD>PHL>KREIRLMKNR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	12.09 RPM
SRP017611_kidney	0.38 RPM	45.38 RPM
SRP017611_liver	0.16 RPM	22.67 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_332 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004733	5 retrocopies	retro_chof_1987, retro_chof_2305, retro_chof_27, retro_chof_462, retro_chof_760,
Erinaceus europaeus	ENSEEUG00000008000	2 retrocopies	retro_eeur_332 , retro_eeur_704,
Homo sapiens	ENSG00000123268	1 retrocopy	retro_hsap_3633,
Mus musculus	ENSMUSG00000023027	1 retrocopy	retro_mmus_3609,
Oryctolagus cuniculus	ENSOCUG00000017023	1 retrocopy	retro_ocun_383,
Otolemur garnettii	ENSOGAG00000026029	1 retrocopy	retro_ogar_1378,
Procavia capensis	ENSPCAG00000010038	2 retrocopies	retro_pcap_303, retro_pcap_442,
Sarcophilus harrisii	ENSSHAG00000004637	2 retrocopies	retro_shar_221, retro_shar_635,