RetrogeneDB ID: retro_eeur_306

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_249141:4837..5309(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1A
• Ensembl ID: ENSEEUG00000010446
• Aliases: None
• Description: RAP1A, member of RAS oncogene family [Source:HGNC Symbol;Acc:9855]

Sequence

>retro_eeur_306
CAGTTTATTCAGGGAATTTTTGTTGAAAAATATGACCAAATGATTGAAGATTTCTAAAGAAAGCAAGTTGAAGTAGACTG
CCAACTGTGTATGCTGGAAGTCCTGGACACAACAGGAACAGAATGATGAGGGATTTATATATGGAGAATGGCCAAGGTTT
TGCACTAGTATATTCTACTACAGCTCAATCCACATTTGACTTACAGGACCTGAGGGAACAGATTTTATGGGTTAAAGACA
CAGAAGATGTTTCACTGATTTTGGTTGACATTAGATGTGATTTGGAAGATGAGCAAGTAGTTGGCAAAGAACAGGGTCAG
AACTGAACAAGAAAATGGTGTAATCTTTTTAGAATCTTCTGCAAAGTCAAAAAGCAATGTTAATGAAAAATTTTATGAGA
CTGTCAGACAGATAAATTGAAAAACATTTAGTGGAAAAGAAAAAGCCTAAAAAGAAATCATGCCTGCTGCTC

Alignment

ORF - retro_eeur_306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.07 %
• Parental protein coverage: 98.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QFVQGIFVEKYDPTIEDSYRKQVEVDCQQCMLEILD-TAGTEQFTAMRDLYMKNGQGFALVYSITAQSTF
          QF.QGIFVEKYD..IED..RKQVEVD...C.L..L....G......MRDLYM.NGQGFALVYS.TAQSTF
Retrocopy QFIQGIFVEKYDQMIEDF*RKQVEVD---CQLCMLE<SPGHNRNRMMRDLYMENGQGFALVYSTTAQSTF

Parental  NDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFL-ESSAKSKINVNEIFY
          .DLQDLREQIL.VKDTEDV..ILV...CDLEDE.VVGKEQGQN..R.WCN.........KS....NE.FY
Retrocopy -DLQDLREQILWVKDTEDVSLILVDIRCDLEDEQVVGKEQGQN*TRKWCNLFRI>SAKSKSNV--NEKFY

Parental  DLVRQINRKT-PVEKKKPKKKSCLLL
          ..VRQIN.KT..VEKKKPKKKSCLLL
Retrocopy ETVRQIN*KT>LVEKKKPKKKSCLLL

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	31.58 RPM
SRP017611_kidney	0.00 RPM	51.39 RPM
SRP017611_liver	0.00 RPM	32.16 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_306 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 21 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005384	1 retrocopy	retro_amel_1764,
Canis familiaris	ENSCAFG00000013686	1 retrocopy	retro_cfam_696,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843, retro_cjac_3844, retro_cjac_728,
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Equus caballus	ENSECAG00000016434	1 retrocopy	retro_ecab_99,
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,
Echinops telfairi	ENSETEG00000016893	2 retrocopies	retro_etel_1196, retro_etel_176,
Homo sapiens	ENSG00000116473	1 retrocopy	retro_hsap_1364,
Myotis lucifugus	ENSMLUG00000010571	3 retrocopies	retro_mluc_2311, retro_mluc_2312, retro_mluc_2313,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327, retro_mdom_139, retro_mdom_1777,
Mus musculus	ENSMUSG00000068798	2 retrocopies	retro_mmus_1963, retro_mmus_3027,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Ochotona princeps	ENSOPRG00000003999	3 retrocopies	retro_opri_321, retro_opri_460, retro_opri_875,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,
Tarsius syrichta	ENSTSYG00000004521	3 retrocopies	retro_tsyr_1546, retro_tsyr_1829, retro_tsyr_2140,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,