RetrogeneDB ID: retro_eeur_466

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_314625:23945..25164(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBAP1
• Ensembl ID: ENSEEUG00000011672
• Aliases: None
• Description: ubiquitin associated protein 1 [Source:HGNC Symbol;Acc:12461]

Sequence

>retro_eeur_466
ATGGTTTCTAAGAAGTTGGGTGCAGATCTTCATGGGACTTTCAGTTACCTTGATGATGTTACATTTAAGATAGGAGACAA
ATTCAAAACACCAGCTAAAGTTGGTCTACCTATTGGCTTCTCCTTGCCTGATTGTTTGCAGGTTGTCAGAGAAGTACAGT
ATGACTTCTCCTTGGAAAAGAAGACCATTGAATGGGCTGAAGATATTAAGAAGATCCAGGGAAGCAAAGCTCAGGGCTGA
AGAAGCTGAGGCTAAAGTGAATTCTAAGAGAGGTCCAGAGGGTGACAGCATAATGAGCTTCTCCAAGACTCACAGTGCAG
CCAGGATGCTGCCTCCCATTAACCCCATCCTCGCCAGCTTACAGCACAACAGAATCCTCACCCCCACTCACATCAGCAGC
AGTGCCATGAAACAGAAAGTCCTCAGCCCACCCCACACCAAGACAGATTTTAACCCAGCTAACTTTGAGTGTGAAGAAGA
CCCATTTGATAATGTGGAGTTAAAAACTATTGATGAGAAGGAGGAACTGAGAAATATTCTGGTAGGAACCACTGGACCCA
TTATGGCTCAGTTATTGGACAGTAATTTGCCCAGAGGAAGCTCTAGGTCTGTATTACAGGACGAGGAGGTCCTGGCATCT
CTGGAGCAGGCCATCCTAGATTCCAAGCCTCTTCACAAACCTAACGGCTTTATAACCTTACCACAATTGGGCAACTGTGA
AAAGATGCCACTGTCTTCCAAAGTGTCCCTGCCCCCTGTCCATGCAGTAAGCAATATTATATCCCTGTCCTTTCCCAAAC
TTGACTCTGATGACAGGAATCAGAAGACCACCAAACTAGCAAACACTTTCTATAGCATATCCTGCTTCCGCAGTGACAAG
TTCCAGAGTTCCCCAAAGCTTTCTACCCAAAGCAGTGCCAGTGAGCTCAATGGGCATCATACTTTTGGACTTTCAGCTTT
GAACTTGGACAGTGGTTCAGAGTTGCCATCTCTGACCCCCTCTGACCTGACTACCCAGATGCCTTCCCTCTCTGTATTGT
CTGTGTGCACAGAAGAGTCATCACCTCCAAATACAGGTTCCATGGTCACACCTACTAATTTTTCAATGTCACAAGTGCTC
AACACGCCAAGCTGTCCCCAAGCTTATTCTGAACTATAGACACTCTCCCCCAGTGAGCAGAAGTGTGTGGAGACAGTGGT
CAACATGGGCTACGCGTAT

Alignment

ORF - retro_eeur_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.83 %
• Parental protein coverage: 80.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASKKLGADLHGTFSYLDDVPFKIGDKFKTPAKVGLPIGFSLPDCLQVVREVQYDFSLEKKTIEWAEDIK
          M.SKKLGADLHGTFSYLDDV.FKIGDKFKTPAKVGLPIGFSLPDCLQVVREVQYDFSLEKKTIEWAEDIK
Retrocopy MVSKKLGADLHGTFSYLDDVTFKIGDKFKTPAKVGLPIGFSLPDCLQVVREVQYDFSLEKKTIEWAEDIK

Parental  KIQ-EAQREAERRAEEAEAKVNSKSGPEGDSKMSFSRTHSAATMPPPINPILASLQHNSILTPTRVSSSA
          KIQ.EA...AE....EAEAKVNSK.GPEGDS.MSFS.THSAA.M.PPINPILASLQHN.ILTPT..SSSA
Retrocopy KIQ>EAKLRAE----EAEAKVNSKRGPEGDSIMSFSKTHSAARMLPPINPILASLQHNRILTPTHISSSA

Parental  MKQKVLSPTHTKADFNPADFECEEDPFDNLELKTIDEKEELRNILVGTTGPIMAQLLDSNLPRGSSGSML
          MKQKVLSP.HTK.DFNPA.FECEEDPFDN.ELKTIDEKEELRNILVGTTGPIMAQLLDSNLPRGSS.S.L
Retrocopy MKQKVLSPPHTKTDFNPANFECEEDPFDNVELKTIDEKEELRNILVGTTGPIMAQLLDSNLPRGSSRSVL

Parental  QDEEVLASLEQATLDFKPLHKPNGFITLPQLGNCEKMPLSSKVSLPPVPAVSNIKSLSFPKLDSDDSNQK
          QDEEVLASLEQA.LD.KPLHKPNGFITLPQLGNCEKMPLSSKVSLPPV.AVSNI.SLSFPKLDSDD.NQK
Retrocopy QDEEVLASLEQAILDSKPLHKPNGFITLPQLGNCEKMPLSSKVSLPPVHAVSNIISLSFPKLDSDDRNQK

Parental  TTKLASTFHSTSCLRSGKSRSSPKPSTQSSASELNGHHTLGLSALNLDSGTEAPSLTPSDLTSQMPSLSV
          TTKLA.TF.S.SC.RS.K..SSPK.STQSSASELNGHHT.GLSALNLDSG.E.PSLTPSDLT.QMPSLSV
Retrocopy TTKLANTFYSISCFRSDKFQSSPKLSTQSSASELNGHHTFGLSALNLDSGSELPSLTPSDLTTQMPSLSV

Parental  LSVCTQESSPPNTGSTVTP-NFSTSQVPNTPSCPQAYSELQTLSPSERQCVETVVNMGYSY
          LSVCT.ESSPPNTGS.VTP.NFS.SQV.NTPSCPQAYSEL.TLSPSE..CVETVVNMGY.Y
Retrocopy LSVCTEESSPPNTGSMVTPTNFSMSQVLNTPSCPQAYSEL*TLSPSEQKCVETVVNMGYAY

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	1.29 RPM	30.46 RPM
SRP017611_kidney	1.50 RPM	45.01 RPM
SRP017611_liver	0.96 RPM	26.69 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_466 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000011672	1 retrocopy	retro_eeur_466 ,
Myotis lucifugus	ENSMLUG00000013063	1 retrocopy	retro_mluc_2305,
Otolemur garnettii	ENSOGAG00000015802	1 retrocopy	retro_ogar_557,
Ochotona princeps	ENSOPRG00000009100	3 retrocopies	retro_opri_355, retro_opri_477, retro_opri_680,
Ictidomys tridecemlineatus	ENSSTOG00000028294	1 retrocopy	retro_itri_1318,
Tarsius syrichta	ENSTSYG00000013035	2 retrocopies	retro_tsyr_1908, retro_tsyr_846,