RetrogeneDB ID: retro_eeur_180

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_176554:6..495(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF1
• Ensembl ID: ENSEEUG00000009255
• Aliases: None
• Description: serine/arginine-rich splicing factor 1 [Source:HGNC Symbol;Acc:10780]

Sequence

>retro_eeur_180
ATGTCAGGAGGTGGTGTTATTCGTGGCCCAGCAGGGAACAACGATTGCCGTATCTACGTGGGCAACTTACCTCCAGACAT
CCGAACCAAGGACATTGAGGACGTGTTTTACAAATAAGGTGCTATCCGTGACATCGACCTCAAGAATAGCCGCGGAGGAC
CGCCCTACGCCTTCGTGGAATTCGAGGATCCGAGAGACGCGGAAGACGCGGTGTACGGTCGCGGCTATGATTACGATGGA
TACTGCTTGCGGGTGGAGTTTCCTCGCGGCCGCGGAACCGACCGAAGCGGCGGTGGGGGTGCAGGTGGTGGAGCTCCCCG
AGGCTGCTATGGCCCCCTGTCCCCGCGTTCTGAAAACAGAGTGGTTGTCTCTGGACTGCCTCCAAGTGGAAATTGGCAGG
ATTTGAAGGATCACATGTGTGAAGCAGGTGATGTATGTTATGCTGATGTTTACCGAGATAACCCTGGTGTCGTGGAGTTT
GTACGGGAA

Alignment

ORF - retro_eeur_180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.7 %
• Parental protein coverage: 56.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA
          MSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYK.GAIRDIDLKN.RGGPP.AFVEFEDPRDAEDA
Retrocopy MSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYK*GAIRDIDLKNSRGGPPYAFVEFEDPRDAEDA

Parental  VYGRDGYDYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDH
          VYGR.GYDYDGY.LRVEFPR.GRGT.R.GGGG.GGGAPRG.YGP.S.RSENRVVVSGLPPSG.WQDLKDH
Retrocopy VYGR-GYDYDGYCLRVEFPR-GRGTDRSGGGGAGGGAPRGCYGPLSPRSENRVVVSGLPPSGNWQDLKDH

Parental  MREAGDVCYADVYRDGTGVVEFVRK
          M.EAGDVCYADVYRD..GVVEFVR.
Retrocopy MCEAGDVCYADVYRDNPGVVEFVRE

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	0.16 RPM	91.69 RPM
SRP017611_kidney	0.00 RPM	141.78 RPM
SRP017611_liver	0.00 RPM	47.75 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_180 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000009255	1 retrocopy	retro_eeur_180 ,
Myotis lucifugus	ENSMLUG00000011040	1 retrocopy	retro_mluc_307,
Ochotona princeps	ENSOPRG00000001234	2 retrocopies	retro_opri_335, retro_opri_625,