RetrogeneDB ID: retro_eeur_160

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_112614:411..957(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRAS
• Ensembl ID: ENSEEUG00000003058
• Aliases: None
• Description: Kirsten rat sarcoma viral oncogene homolog [Source:HGNC Symbol;Acc:6407]

Sequence

>retro_eeur_160
ATGACTGAGTACAAACTGGCGGTGGTCGGAGCAGGTGGTGTTGGGAAAAACGCACTTACAATCCAACTAATCCAGAACCA
CTTTGTAGATGAATATGATCCCACCATAGAGGATTCTTACCGTAAACAGGTGGTTAGAGATGGGGAAACCTGTCTGTTGG
ACATACTGGATACAGCTGGACAAGAAGAATACAGTGCCATGAGAGACCAATACATGAGAACAGGCGAATGGTTCCTTTGT
GTATTTGCCATCAATAATAGCAAATCATTTGCAGATATTAACCTCTACAGGGAACAGATTAAGTGAGTAAAAGACTCAGA
TGATGTACCTATGGTGCTAGTAGGAAATAAGTGTGACTTGCCAACAAGAACAGTTGACACGAAACAAGCCCATGAGCTGG
CCAAGAGTTATGGGATTCCATTCATTGAAACCTCAGCCAAGACCAGACAGGGTGTTGAAGATGCCTTTTACACACTGGTA
AGAGAGATACGTCAGTACCGAATGAAAAAACTCAACAGCAGTGATGATGGCACACAAGGCTGTATG

Alignment

ORF - retro_eeur_160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 95.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTEYKLVVVGAGGVGKSALTIQLIQ-HFVDEYDPTIEDSYREQVVIDGETCLLDILDTAGQEEYSAMRDQ
          MTEYKL.VVGAGGVGK.ALTIQLIQ.HFVDEYDPTIEDSYR.QVV.DGETCLLDILDTAGQEEYSAMRDQ
Retrocopy MTEYKLAVVGAGGVGKNALTIQLIQNHFVDEYDPTIEDSYRKQVVRDGETCLLDILDTAGQEEYSAMRDQ

Parental  YMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIP
          YMRTGE.FLCVFAINN.KSF.DI..YREQIK.VKDS.DVPMVLVGNKCDLP.RTVDTKQA..LA.SYGIP
Retrocopy YMRTGEWFLCVFAINNSKSFADINLYREQIK*VKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIP

Parental  FIETSAKTRQRVEDAFYTLVREIRQYRLKKIN-KEEKTPGCV
          FIETSAKTRQ.VEDAFYTLVREIRQYR.KK.N.....T.GC.
Retrocopy FIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQGCM

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	8.06 RPM	34.32 RPM
SRP017611_kidney	11.44 RPM	8.81 RPM
SRP017611_liver	2.57 RPM	13.83 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_160 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011469	1 retrocopy	retro_dord_520,
Erinaceus europaeus	ENSEEUG00000003058	1 retrocopy	retro_eeur_160 ,
Erinaceus europaeus	ENSEEUG00000010052	1 retrocopy	retro_eeur_327,
Erinaceus europaeus	ENSEEUG00000010446	2 retrocopies	retro_eeur_306, retro_eeur_361,
Homo sapiens	ENSG00000133703	1 retrocopy	retro_hsap_3474,
Macaca mulatta	ENSMMUG00000015381	1 retrocopy	retro_mmul_1766,
Monodelphis domestica	ENSMODG00000017458	1 retrocopy	retro_mdom_153,
Nomascus leucogenys	ENSNLEG00000005266	1 retrocopy	retro_nleu_338,
Tupaia belangeri	ENSTBEG00000003830	2 retrocopies	retro_tbel_2242, retro_tbel_271,