RetrogeneDB ID: retro_eeur_195

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_204842:8414..9222(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM76B
• Ensembl ID: ENSEEUG00000008119
• Aliases: None
• Description: family with sequence similarity 76, member B [Source:HGNC Symbol;Acc:28492]

Sequence

>retro_eeur_195
GCCTGCACCAAGTGCACCCAGCGCTACCCCTTTGAGGAACTCTCCTAGGGCCAGCAGCTCTGCAAGGAATGTCGGATTGT
GCACCAGATCATCGTCAAGTGCACCTACTGCAGGTCGGAGTTCCAGCAGGAGAGCAAAACTAACACAATTTGTAAGAAGT
GTGCTCAAAATGTGAAACAGTTTGGCACGCCCAAGCCTTATCAGTACTGTAACATAATCGCAGCATTCATTGGCACAAAG
TGTCAGAGATGCACAAATTTAGAGAAAAAGTACGGACCGCCTCAGACCTGCGAGCAGTGCAAGCAGTAGTGTGCTTTCGA
TCGGAAAGAAGAAGGAAGAAGAAAGGTTGATGGGAAGTTGTTGTGCTGGCTCTACTTTATCATACAAGAGAGTTTTACAG
AAGACAAAAGAACAGAGGAAGAGCCTGGGATGTCACATTCAAATTCCTCTTCTTTCATCCCTCACCAAGAAAGACCAGCA
TCAGTCAAAGCACAATCACCACCACCACCACCATCACCACCATCACAGCAGTAGCCATCACAAAATTAGCAACCTGAGTC
CAGAACAAGAGCAGGGACTGTGGAAACAGAGCCATAAATCCTCTGCAACAATTGAGAATGAAACTCCAAAGAAAAAGCCC
AAATTGGAATCTAAGCCATCTAATGGAGATAGTAACTCTATAAATCAGTCAGCAGATAGTGGGGGAACAGACAGTTTTGT
CCTCATAAGTCAACTGAAGGAAGAAGTGACATCACTTAAGTGTCTCTTACAGCAGAGAGACCAGGCCATCTTAGAGAAAG
ATAAAAAG

Alignment

ORF - retro_eeur_195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.17 %
• Parental protein coverage: 97.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ACTKCTQRYPFEELSQGQQLCKECRIAHPI-VKCTYCRSEFQQEXXXXXXXXXXXXXXXXXXXPKPCQYC
          ACTKCTQRYPFEELS.GQQLCKECRI.H.I.VKCTYCRSEFQQE...................PKP.QYC
Retrocopy ACTKCTQRYPFEELS*GQQLCKECRIVHQIIVKCTYCRSEFQQESKTNTICKKCAQNVKQFGTPKPYQYC

Parental  NIIAAFIGTKCQRCTNSEKKYGPPQTCEQCKQQCAFDRKEEGRRKVDGKLLCWLCTLSYKRVLQKTKEQR
          NIIAAFIGTKCQRCTN.EKKYGPPQTCEQCKQ.CAFDRKEEGRRKVDGKLLCWL............K...
Retrocopy NIIAAFIGTKCQRCTNLEKKYGPPQTCEQCKQ*CAFDRKEEGRRKVDGKLLCWLYFI-IQESFTEDKRTE

Parental  KSLGSSHSNSSS-SSLTEKDQHHSKHHHHHHHHHHRHSSSHHKISNLSPEQEQGLWKQSHKSSATIQNET
          ...G.SHSNSSS.SSLT.KDQH.SK............SSSHHKISNLSPEQEQGLWKQSHKSSATI.NET
Retrocopy EEPGMSHSNSSS>SSLTKKDQHQSKXXXXXXXXXXXXSSSHHKISNLSPEQEQGLWKQSHKSSATIENET

Parental  PKKKPKLS---PSGDSSSINQSADSGGTDNFVLISQLKEEVTSLKRLLQQRDQAILEKDKK
          PKKKPKL......GDS.SINQSADSGGTD.FVLISQLKEEVTSLK.LLQQRDQAILEKDKK
Retrocopy PKKKPKLESKPSNGDSNSINQSADSGGTDSFVLISQLKEEVTSLKCLLQQRDQAILEKDKK

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	5.96 RPM	12.73 RPM
SRP017611_kidney	3.75 RPM	12.38 RPM
SRP017611_liver	0.48 RPM	3.05 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_195 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008119	1 retrocopy	retro_eeur_195 ,
Oryctolagus cuniculus	ENSOCUG00000014549	1 retrocopy	retro_ocun_593,