RetrogeneDB ID: retro_eeur_371

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_272863:10259..12105(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABCB6
• Ensembl ID: ENSEEUG00000007653
• Aliases: None
• Description: ATP-binding cassette, sub-family B (MDR/TAP), member 6 [Source:HGNC Symbol;Acc:47]

Sequence

>retro_eeur_371
CTGCCCGGGTACCTCCTGTCGGCCGCCTTCTTGGAGACATTGGCGGGCGCCTGCGGCCTGGGGCTGCTGATGGCGGAGCG
CAGGAGCGCGCTGCAGAAACTCGCCATGGGCGTGCGGGTGCGGTGCGGGCACAGCCCCGGGCTGCTGCTGCTCTGGACCG
TGATGTTCGCCGCCCAGAACTTGGCGCTGGTGTCCTGGAAGAGCCCGCAGTGGTGGTGAGCAAGGGCGGACCTGGGCCAG
CAGGTTCAGTTTGGCCTGTGGGCACTGCGGTATGTGGTGTCTGGGGGGCTTTTTCTCCTGGGGCTCTGGGCCCCTGGACT
GCGACCCCAGACATACACCTTGCGGGTCAATGAAGAGGATCAGGATGTAGAGAGAAGCCAGGTTCCCTCAACCCAGGGGT
CATCTCCATCTACCTGGGGTGACCTTGGCAGGAAGCTCCGCCTCCTAAGTGGCTATCTGTGGCCTCGGGGGAGCCCTGCC
CTGCAGCTAGTGGTGCTCTGCTGCCTGGGACTCATGGGGCTGGACCGGGGATTGAACGTGCTGGTCCCCATCTTCTACAG
AGACATAGTGAACTTGCTGACAGAGAAGGCCCCTTGGAACTCCCTGGCCTGGACCGTCACCACTTATGTCTTCCTCAAGT
TCCTGCAGGGGGGCGGCACTGGCAATACAGGCTTCGTGAGCAACCTTCCTCTGAATCCGGGTCCAGCAGTACACCTCTCG
CCGCGTGGAGCTGCGTCTCTTCTGCCACCTGCATGAGTTGTCACTGCGCTGGCACCTGGGTCGCCTCACAGGGGAAGTGC
TGCGGGTCGTGGACCGGGGCACATCCAGCGTCACTGGGCTGCTCAGTTACCTGGTATTCAACATCATCCCCACGCTGGCC
GACATCATCATTGGCATCATCTACTTCAGCATGTTCTTCAACGCCTGGTTTGGCCTCATCGTCTTCCTGTGCATGAGCCT
CTACCTCATCCTGACCATTGTGGTCACCGAGTGGAGAACTAAGTTCCGACGTGACATGAACATGCAGGAGAATGCTACCC
GGGCACGAGCCGTGGACTCCCTGTTGAACTTTGAGACGGTGAAGTATTACAATGCAGAAGGCTATGAAGTGGAGCGCTAC
CAAGAGGCCATCATCAAGTACCAGGGTTTGGAGTGGAAGTCAAGTGCTTCATTGGTTTTGCTGAATCAGACCCAGAACCT
GGTGATTGGCCTCGGGCTCCTGGCCGGCTCCCTGCTGTGTGCATTCTTTGTCAGCGAGCAGAAGCTGCAGCTCGGGGACT
TTGTGCTCTTTGGCACCTACATCATTCAGCTCTACATGCCCCTCAACTGGTTTGGCACCTACTACAGGATGATCCAGACT
AACTTCATCGACATGGAGAACATGTTTGATCTGCTCAAAGAGGAGGCAGAAGTGAAGGACCTCCCTGGCGCAGGGCCCCT
TCACTTCCAGAAGGGCCAGATCGAGTTTGAAAACGTGCACTTCAGCTATACAGATGGACGGGAGACCCTGCAAGACATGT
CCTTCACTGTGATGCCTGGCCAGACACTAGCCCTGGTGGGCCCGACCGGCGCAGGGAAGAGCACCATCCTGCGCCTGCTC
TTCCGCTTCTATGACATCAACAGTGGCTGTATCCGCATCGATGGGCAGGACATCTCCAAGGTAACCCAGACCTCCCTGCG
GTCCCACATTGGAGTTGTGCCACAGGACACCGTCCTCTTCAATGACACCATTGCCAACAACATCCGCTATGGCCGCATCA
CAGCTGATGCTGCTGAGGTGGAGGCAGCCGCCAAGGCTGCAGGCATCCATGAAGCCATCCTGGCTTTCCCCGAAGGCTAC
GAGACA

Alignment

ORF - retro_eeur_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.77 %
• Parental protein coverage: 69.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPGYLLSAAFLETLAGACGLGLLLAERRSALQKLAMGVRVRCGHSPGLLLLWTVTFAAQNLVLVSWKSPQ
          LPGYLLSAAFLETLAGACGLGLL.AERRSALQKLAMGVRVRCGHSPGLLLLWTV.FAAQNL.LVSWKSPQ
Retrocopy LPGYLLSAAFLETLAGACGLGLLMAERRSALQKLAMGVRVRCGHSPGLLLLWTVMFAAQNLALVSWKSPQ

Parental  WWWARADLGQQVQFGLWALRYVVSGGLFLLGLWAPGLRPQTYTLRVNEEDQDVERSQVPSTQGSSRSTWG
          WW.ARADLGQQVQFGLWALRYVVSGGLFLLGLWAPGLRPQTYTLRVNEEDQDVERSQVPSTQGSS.STWG
Retrocopy WW*ARADLGQQVQFGLWALRYVVSGGLFLLGLWAPGLRPQTYTLRVNEEDQDVERSQVPSTQGSSPSTWG

Parental  DLGRKLRLLSGYLWPRGSPALQLVVLCCLGLMGLDRGLNVLVPIFYRDIVNLLTEKAPWNSLAWTVTTYV
          DLGRKLRLLSGYLWPRGSPALQLVVLCCLGLMGLDRGLNVLVPIFYRDIVNLLTEKAPWNSLAWTVTTYV
Retrocopy DLGRKLRLLSGYLWPRGSPALQLVVLCCLGLMGLDRGLNVLVPIFYRDIVNLLTEKAPWNSLAWTVTTYV

Parental  FLKFLQGGGTGSTG-FVSNLRTFLWIRVQQYTSRRVELRLFCHLHELSLRWHLGRRTGEVLRVVDRGTSS
          FLKFLQG...G.TG.......TFL.IRVQQYTSRRVELRLFCHLHELSLRWHLGR.TGEVLRVVDRGTSS
Retrocopy FLKFLQG---GGTG>IQAS*ATFL*IRVQQYTSRRVELRLFCHLHELSLRWHLGRLTGEVLRVVDRGTSS

Parental  VTGLLSYLVFNIIPTLADIIIGIIYFSMFFNAWFGLIVFLCMSLYLILTIVVTEWRTKFRRDMNMQENAT
          VTGLLSYLVFNIIPTLADIIIGIIYFSMFFNAWFGLIVFLCMSLYLILTIVVTEWRTKFRRDMNMQENAT
Retrocopy VTGLLSYLVFNIIPTLADIIIGIIYFSMFFNAWFGLIVFLCMSLYLILTIVVTEWRTKFRRDMNMQENAT

Parental  RARAVDSLLNFETVKYYNAEGYEVERYQEAIIKYQGLEWKSSASLVLLNQTQNLVIGLGLLAGSLLCAFF
          RARAVDSLLNFETVKYYNAEGYEVERYQEAIIKYQGLEWKSSASLVLLNQTQNLVIGLGLLAGSLLCAFF
Retrocopy RARAVDSLLNFETVKYYNAEGYEVERYQEAIIKYQGLEWKSSASLVLLNQTQNLVIGLGLLAGSLLCAFF

Parental  VSEQKLQVGDFVLFGTYIIQLYMPLNWFGTYYRMIQTNFIDMENMFDLLKEEAEVKDLPGAGPLHFQKGQ
          VSEQKLQ.GDFVLFGTYIIQLYMPLNWFGTYYRMIQTNFIDMENMFDLLKEEAEVKDLPGAGPLHFQKGQ
Retrocopy VSEQKLQLGDFVLFGTYIIQLYMPLNWFGTYYRMIQTNFIDMENMFDLLKEEAEVKDLPGAGPLHFQKGQ

Parental  IEFENVHFSYTDGRETLQDMSFTVMPGQTLALVGPSGAGKSTILRLLFRFYDINSGCIRIDGQDISKVTQ
          IEFENVHFSYTDGRETLQDMSFTVMPGQTLALVGP.GAGKSTILRLLFRFYDINSGCIRIDGQDISKVTQ
Retrocopy IEFENVHFSYTDGRETLQDMSFTVMPGQTLALVGPTGAGKSTILRLLFRFYDINSGCIRIDGQDISKVTQ

Parental  TSLRSHIGVVPQDTVLFNDTIANNIRYGRITADAAEVEAAAKAAGIHEAILAFPEGYET
          TSLRSHIGVVPQDTVLFNDTIANNIRYGRITADAAEVEAAAKAAGIHEAILAFPEGYET
Retrocopy TSLRSHIGVVPQDTVLFNDTIANNIRYGRITADAAEVEAAAKAAGIHEAILAFPEGYET

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	6.28 RPM	29.81 RPM
SRP017611_kidney	12.00 RPM	49.89 RPM
SRP017611_liver	3.54 RPM	12.54 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_371 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007653	1 retrocopy	retro_eeur_371 ,