RetrogeneDB ID: retro_eeur_649

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_374768:1220..2092(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000003334
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000013364
• Aliases: None
• Description: None

Sequence

>retro_eeur_649
TTTGCTTCCCTGGAGAATAGTGAAAAGGCCTACAATAAACACACAGAAAAAGAATAAGGGCAAAGGACCATTCGAAATCT
TCCATAAGTAGCCGAGCTAAAGTTAGAACCCACTTATGATCCCCCTAGAAAAGCTTCATGGTTATGCAGAGTCCAGGTCC
CTATGATAGGCCATGGACTGGCAGAGGCTATAACCACCATGGTAGAGGGACTGGCTTTGAAAAGGATGAGCCGGGTGCTT
ATGGTGGAGGGTATGGAGGCTATGATGACTCCGGTGGTTATAATGATGGGTATGGCTTTGGGTCTGACAGATTTGGAAGA
GACCTTAATTCCTGCTTTTCAGGAAAGTCTGACCATAGATATGGAGATGGTGGGTCCAGTTTCCAGAGCACCACAGCGCA
CTCTGTACACATGAGGGGATTACCTTACAGAGCTACTGAGAATGATATTTACAATTTTTTCTCTCCTCTTAATCCCATGA
GAGTACACATTGAAATTGGACCCGATGGCAGAGTTACTGGTGAGGCAGATGTTGAATCCGCTACCCATGAAGATGCTGTG
GCAGCTATGGCAAAAGACAAAGCTAATATGCAACATAGATATGTGGAGCTCTTCCTGAATTCTACTGCAGGAACGAGTGG
AGGAGCTTATGATCACAGCTATGTAGAGCTCTTCCTGAACTCTACAGCAGGGGCCAGTGGTGGCGCTTATGGAAGCCAAA
TGATGGGAGGGATGGGCTTGTCCAACCAGTCTAGTTACGGGGGTCCTGCTAGCCAGCAGCTGAGTGGTGGTTATGGAGGT
GGTTACGGTGGTCAGAGCAGTATGAGTGGATACGACCAAGTTCTGCAGGAAAACTCCAGTGACTATCAGTCC

Alignment

ORF - retro_eeur_649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.82 %
• Parental protein coverage: 79.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FASQEIAEKALKKHKERI-GHRYI-EIFK-SSRAEVRTHY-DPPRKLMAMQRPGPYDRPGAGRGYNSIGR
          FAS.E..EKA..KH.E...G.R.I.EIF..SSRA.VRTH...P....M.MQ.PGPYDRP..GRGYN..GR
Retrocopy FASLENSEKAYNKHTEKE*GQRTI>EIFH>SSRAKVRTHL*SP*KSFMVMQSPGPYDRPWTGRGYNHHGR

Parental  GAGFERMRRGAYGGGYGGSGDYGGYDDGYGFGSDRFGRDLNYCFSGMSDHRYGDGGSTFQSTTGHCVHMR
          G.GFE....GAYGGGYGG..D.GGY.DGYGFGSDRFGRDLN.CFSG.SDHRYGDGGS.FQSTT.H.VHMR
Retrocopy GTGFEKDEPGAYGGGYGGYDDSGGYNDGYGFGSDRFGRDLNSCFSGKSDHRYGDGGSSFQSTTAHSVHMR

Parental  GLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNST
          GLPYRATENDIYNFFSPLNP.RVHIEIGPDGRVTGEADVE.ATHEDAVAAM.KDKANMQHRYVELFLNST
Retrocopy GLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVESATHEDAVAAMAKDKANMQHRYVELFLNST

Parental  AGASGGAYEHRYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGGYGGGYGGQSSMSGYG
          AG.SGGAY.H.YVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGGYGGGYGGQSSMSGY.
Retrocopy AGTSGGAYDHSYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGGYGGGYGGQSSMSGYD

Parental  SQGTVNSSYYSS
          .....NSS.Y.S
Retrocopy QVLQENSSDYQS

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	62.36 RPM	170.49 RPM
SRP017611_kidney	44.82 RPM	233.67 RPM
SRP017611_liver	20.10 RPM	93.25 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_649 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003841	4 retrocopies	retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Equus caballus	ENSECAG00000014429	1 retrocopy	retro_ecab_94,
Erinaceus europaeus	ENSEEUG00000010991	1 retrocopy	retro_eeur_481,
Erinaceus europaeus	ENSEEUG00000013364	2 retrocopies	retro_eeur_478, retro_eeur_649 ,
Echinops telfairi	ENSETEG00000011303	1 retrocopy	retro_etel_50,
Loxodonta africana	ENSLAFG00000015766	2 retrocopies	retro_lafr_366, retro_lafr_74,
Myotis lucifugus	ENSMLUG00000016625	1 retrocopy	retro_mluc_124,
Macaca mulatta	ENSMMUG00000010843	1 retrocopy	retro_mmul_2,
Monodelphis domestica	ENSMODG00000009436	3 retrocopies	retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Ochotona princeps	ENSOPRG00000003513	1 retrocopy	retro_opri_11,
Procavia capensis	ENSPCAG00000006715	1 retrocopy	retro_pcap_4,
Pteropus vampyrus	ENSPVAG00000007670	1 retrocopy	retro_pvam_23,
Sorex araneus	ENSSARG00000003024	1 retrocopy	retro_sara_29,
Sarcophilus harrisii	ENSSHAG00000018204	1 retrocopy	retro_shar_674,
Vicugna pacos	ENSVPAG00000007485	2 retrocopies	retro_vpac_594, retro_vpac_614,