RetrogeneDB ID: retro_eeur_494

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_326833:3636..4180(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000013031
• Aliases: None
• Description: None

Sequence

>retro_eeur_494
GTGGTGATGGTTAGTAGGGACCTCTTCAGCACTGGGTAGCTCGTCAGGTCGGCTGACCTCACCCTGGGCCCTGAGAAGTG
CAAGCCGCTGGCTGCTCTGGACTACGAGGTCAAGTTTGAGGTGGGGCTGTATGAGTGTGATACTCGTGCACAGGTGACCC
AGGATTTGCTGGTGTACAGCACCTTCGTGCTCCACAAGCCCTGCCCTGTGGGCAATCTGTCTGCCCTCAGGACCAGCCCT
ATGCAGGTGGCCATAGAATGCTGCTACCCCAGGCAGGGTAACATGAGCAGCCAGCCCATCCTACCCACTTGGCTGTCCTT
ACCACACCACCATCTCGGCAGAGGAGAGGCTCGTTTTCTCCCTGAAGCTCGTGGAAGAAGACTGGAGCACCAAGAAGTTC
TCCACCTTCCGGCTGGGGGACACAGCCCACCCGCAGGCCCAGATTCACACCGCCATCCATGTGCCCCTGATGCTGTTTGT
GGACCACTGTGTGGCAACTCCCACCCCTGACCAGACTGGCCCCCGGCACCACATCATCGTGGAC

Alignment

ORF - retro_eeur_494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.05 %
• Parental protein coverage: 80.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVTVSRDLFGTGKLIRPEDLTLGPEKCKPLVALDSEVKFEVGLHECGNRVQVTQDTLVYSTFLLHEPRPA
          VV.VSRDLF.TG.L.R..DLTLGPEKCKPL.ALD.EVKFEVGL.EC..R.QVTQD.LVYSTF.LH.P.P.
Retrocopy VVMVSRDLFSTG*LVRSADLTLGPEKCKPLAALDYEVKFEVGLYECDTRAQVTQDLLVYSTFVLHKPCPV

Parental  RNLSVLRTSPVQVAIECRYPRQGNVSSRPILPTWL-PFHTTILAEEHLAFSLKLMEEDWSTEKKSPTFRL
          .NLS.LRTSP.QVAIEC.YPRQGN.SS.PILPTWL.P.HTTI.AEE.L.FSLKL.EEDWST.KK..TFRL
Retrocopy GNLSALRTSPMQVAIECCYPRQGNMSSQPILPTWL>PYHTTISAEERLVFSLKLVEEDWST-KKFSTFRL

Parental  GDTAHLQAQVHTGSHVPLRLFVDRCVATPTRDQTGLPHHTIVD
          GDTAH.QAQ.HT..HVPL.LFVD.CVATPT.DQTG..HH.IVD
Retrocopy GDTAHPQAQIHTAIHVPLMLFVDHCVATPTPDQTGPRHHIIVD

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 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_494 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013031	1 retrocopy	retro_eeur_494 ,
Monodelphis domestica	ENSMODG00000013650	1 retrocopy	retro_mdom_1439,
Sarcophilus harrisii	ENSSHAG00000016866	1 retrocopy	retro_shar_385,