RetrogeneDB ID: retro_eeur_577

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_347210:51969..52479(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNJ
• Ensembl ID: ENSEEUG00000002270
• Aliases: None
• Description: cyclin J [Source:HGNC Symbol;Acc:23434]

Sequence

>retro_eeur_577
GAGTTGAAGTTGCCCTCCTACAAAGGCCAGTCCCCTCAACTTAGTCTCCGAAGATATTTTGCTGACTTGATTGCCATCGT
GAGCAATCGCTTCACACTCTGCCCTTCTGCCCGACACCTTGCTGTCTATTTGCTGGACCTGTTTATGGATCGGTATGACA
TCTCTATCCAGCAGCTACACCTAGTTGCACTTTCATGTCTGCTCCTAGCAAGTAAATTTGAAGAGAAAGAAGACAGTGTG
CCTAAGCTGGAGCAGCTCAATAGCCTGGGTTGTATGACTAATGTGAATCTAGTCTTAACAAAGCAGAATTTGCTACATAT
GGAACTATTATTGTTAGAAACCTTTCAGTGGAACCTCTGCCTTCCAACAGCTGCCCATTTCATCGAGTACTATCTCTCCG
AAGAAGTACATGAAACAGATCTTCATGATGGCTGGCCGATGATTTGCTTGGAAAAAACTAAGCTCTACATGGCCAAGTAC
GCAGATTACTTCCTGGAAGTGTCTTTGCAA

Alignment

ORF - retro_eeur_577 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.82 %
• Parental protein coverage: 66.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELKLPSYKGQSPQLSLRRYFADLIAIVSNRFTLCPSARHLAVYLLDLFMDRYDISIQQLHLVALSCLLLA
          ELKLPSYKGQSPQLSLRRYFADLIAIVSNRFTLCPSARHLAVYLLDLFMDRYDISIQQLHLVALSCLLLA
Retrocopy ELKLPSYKGQSPQLSLRRYFADLIAIVSNRFTLCPSARHLAVYLLDLFMDRYDISIQQLHLVALSCLLLA

Parental  SKFEEKEDSVPKLEQLNSLGCMTNMNLVLTKQNLLHMELLLLETFQWNLCLPTAAHFIEYYLSEAVHETD
          SKFEEKEDSVPKLEQLNSLGCMTN.NLVLTKQNLLHMELLLLETFQWNLCLPTAAHFIEYYLSE.VHETD
Retrocopy SKFEEKEDSVPKLEQLNSLGCMTNVNLVLTKQNLLHMELLLLETFQWNLCLPTAAHFIEYYLSEEVHETD

Parental  LHDGWPMICLEKTKLYMAKYADYFLEVSLQ
          LHDGWPMICLEKTKLYMAKYADYFLEVSLQ
Retrocopy LHDGWPMICLEKTKLYMAKYADYFLEVSLQ

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	0.32 RPM	1.77 RPM
SRP017611_kidney	0.56 RPM	0.75 RPM
SRP017611_liver	0.32 RPM	2.25 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_577 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016259	1 retrocopy	retro_cjac_3274,
Erinaceus europaeus	ENSEEUG00000002270	2 retrocopies	retro_eeur_535, retro_eeur_577 ,
Homo sapiens	ENSG00000107443	1 retrocopy	retro_hsap_3850,
Gorilla gorilla	ENSGGOG00000006034	1 retrocopy	retro_ggor_2595,
Oryctolagus cuniculus	ENSOCUG00000011114	1 retrocopy	retro_ocun_425,
Tarsius syrichta	ENSTSYG00000009466	1 retrocopy	retro_tsyr_741,