RetrogeneDB ID: retro_eeur_322

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_253560:4048..4942(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: B4GALT7
• Ensembl ID: ENSEEUG00000004216
• Aliases: None
• Description: xylosylprotein beta 1,4-galactosyltransferase, polypeptide 7 [Source:HGNC Symbol;Acc:930]

Sequence

>retro_eeur_322
ATGTTCCCCTCCAGGAGGAAGGCGATGCAGCTGCCCTGGCAGGACAGCAGGTCCAGGTTGCTCCCCAGCGGCCTCCCCAG
GAAGTGCTCTGTCTTCCACCTCTTTGTGGCCTGTCTTTTACTGGGCTTCCTCTCTGGCTGCGGCTTAGCTGCTCTGGTGA
CATGGCCCGGGCAGCCAGGGGACAAGGACAGGAGACCCCAGGCCCGTCCCGGGCCTGTCCCCCAGAGCTGCCGCCTGAGC
ACTGGGAAGAAGACCCGTCTTGGGGCCCCCACCGCCTAGCAGTGCTGGTGCCCTTCCGGGAACGCTTCGAGGAGCAGCTA
GTCTTCGTAATCCACATGCACCGCTTTCTGAGCCGGAAGAAGATCCAGCACCACATCTATGTGCTCAATCAGGTGGACCA
CTTCAGGTTCAACAGGGCAGTACTCATCAGTGTGGGCTTCCTGGAGAGCAGCAACACCACCGACTACATCGCCATGCACA
ACGTGGATCTGCTGCCCCTTAACGAGGAGCTGGACTATGGCTTCTCCGAGGCCGGGTCCTTCCACGTGCCTTCCCCTGAG
CTGCACCAGCTCTATCACTACAAGACCTAAGTGGGCGGCATCCTGCTGCTGTCCAAGCAGCACTACCAGCTGTGCAAGGA
ATGTCCAATCGCTTCTGGGGTTGGGGCCGCAAGGATGATGAGTTCTACCGGCGCATCAAAGGAGCGGGGCTCCAGATCCT
CCGGCCCTCAGAAATCAAAACTGTATACAAGACGTTCCACCACTTGCATAACCCTGCCTGGCGGAAGAGGGACCAGAAGC
GCATTGCCGCGCAGAAGCAGGAACAGTTCAAGGTGGACCTCGAGGGCGGCCTCAACAGGTCAAGTACAGAGTGGACTCCC
GGACAGCCCTGTCT

Alignment

ORF - retro_eeur_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 92.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFPSRRKAVQLPWQDGRSRLLPSSLPRKCSVFHLFVACLLLGFLS-LLWLQLSCSGDMARAARGQGQETP
          MFPSRRKA.QLPWQD.RSRLLPS.LPRKCSVFHLFVACLLLGFLS..L.L..S.....A....GQ..ETP
Retrocopy MFPSRRKAMQLPWQDSRSRLLPSGLPRKCSVFHLFVACLLLGFLS<WLRLSCSGDMARAARGQGQ--ETP

Parental  GPSRACPPELPPEHWEEDPSWGPHRLAVLVPFRERFEELLVFVPHMHRFLSRKKIQHHIYVLNQVDHFRF
          GPSRACPPELPPEHWEEDPSWGPHRLAVLVPFRERFEE.LVFV.HMHRFLSRKKIQHHIYVLNQVDHFRF
Retrocopy GPSRACPPELPPEHWEEDPSWGPHRLAVLVPFRERFEEQLVFVIHMHRFLSRKKIQHHIYVLNQVDHFRF

Parental  NRAALINVGFLESSNTTDYIAMHDVDLLPLNEELDYGFPEAGPFHVASPELHPLYHYKTYVGGILLLSKQ
          NRA.LI.VGFLESSNTTDYIAMH.VDLLPLNEELDYGF.EAG.FHV.SPELH.LYHYKT.VGGILLLSKQ
Retrocopy NRAVLISVGFLESSNTTDYIAMHNVDLLPLNEELDYGFSEAGSFHVPSPELHQLYHYKT*VGGILLLSKQ

Parental  HYRLC-NGMSNRFWGWGREDDEFYRRIKGAGLQVLRPSEIKTGYKTFRHLHDPAWRKRDQKRIAAQKQEQ
          HY.LC..GMSNRFWGWGR.DDEFYRRIKGAGLQ.LRPSEIKT.YKTF.HLH.PAWRKRDQKRIAAQKQEQ
Retrocopy HYQLC<QGMSNRFWGWGRKDDEFYRRIKGAGLQILRPSEIKTVYKTFHHLHNPAWRKRDQKRIAAQKQEQ

Parental  FKVDREGGLN-TVKYRVDSRTALS
          FKVD.EGGLN..VKYRVDSRTALS
Retrocopy FKVDLEGGLN<QVKYRVDSRTALS

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	0.48 RPM	8.54 RPM
SRP017611_kidney	0.19 RPM	11.06 RPM
SRP017611_liver	0.16 RPM	8.20 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_322 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	ENSEEUG00000004216	1 retrocopy	retro_eeur_322 ,