RetrogeneDB ID: retro_eeur_377

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_275315:18224..18764(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBDC1
• Ensembl ID: ENSEEUG00000001116
• Aliases: None
• Description: polysaccharide biosynthesis domain containing 1 [Source:HGNC Symbol;Acc:28790]

Sequence

>retro_eeur_377
ATGGAGGCGACTACAAGAATGGAGGATTCGGTTTCCGGGGAATTGGTGTCAGTAGCACATGCTCTTTCTCTCCCAGCTGA
ATCTTACGGCAATGATCCTGATATTGAGATGGCTTGGGCCATGAAAGCCATGCAACATGCTGAGGTCTACTACACCCTTA
TTTCATCAGTTGACCCACAGTTTCCGAAACTCACGAAAGTTGATGACCAAATTTATTCTGAATTTCGGGAACGATTTGAG
AATCTCAGGGTAGATGTATTGGACCCAGAAGAGCTGAAATCAGAATCAGCTAAAGAGAAATGGAGGCCATTCTGCTTGAA
ATTTGATGAGATTGTAGAAGATTTCAACTATGGTACTTTACTGCGACTGGATTGTTCTCAAGGCTACACTGAAGAAAATA
CCATCTTTGCCCCCAGAATACAGTTTTTTGCCATTGAAATTGCTCGAAATCGGGAAGGCTGTAACAAAGCAGTTTACATT
AGTGTTCAGGACAAAGAAGAGAAAGGAACCAGTGATGAAGAAGAAAGTAGAACTCAGAGT

Alignment

ORF - retro_eeur_377 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.78 %
• Parental protein coverage: 86.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEATKRMEDSVSGELVSVAHALSLPAESYGNDPDIEMAWAMKAMQHAEVYYKLISSVDPQFLKLTKVDDQ
          MEAT.RMEDSVSGELVSVAHALSLPAESYGNDPDIEMAWAMKAMQHAEVYY.LISSVDPQF.KLTKVDDQ
Retrocopy MEATTRMEDSVSGELVSVAHALSLPAESYGNDPDIEMAWAMKAMQHAEVYYTLISSVDPQFPKLTKVDDQ

Parental  IYSEFRERFENLRVDVLDPEELKSESAKEKWRPFCLKFDGIVEDFNYGTLLRLDCSQGYTEENTIFAPRI
          IYSEFRERFENLRVDVLDPEELKSESAKEKWRPFCLKFD.IVEDFNYGTLLRLDCSQGYTEENTIFAPRI
Retrocopy IYSEFRERFENLRVDVLDPEELKSESAKEKWRPFCLKFDEIVEDFNYGTLLRLDCSQGYTEENTIFAPRI

Parental  QFFAIEIARNREGCNKAVYISVQDKEEKGTSDEEESRTQS
          QFFAIEIARNREGCNKAVYISVQDKEEKGTSDEEESRTQS
Retrocopy QFFAIEIARNREGCNKAVYISVQDKEEKGTSDEEESRTQS

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	1.61 RPM	14.02 RPM
SRP017611_kidney	2.06 RPM	18.00 RPM
SRP017611_liver	1.77 RPM	9.32 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_377 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017228	2 retrocopies	retro_cfam_1588, retro_cfam_944,
Callithrix jacchus	ENSCJAG00000018571	1 retrocopy	retro_cjac_1880,
Equus caballus	ENSECAG00000009882	1 retrocopy	retro_ecab_532,
Erinaceus europaeus	ENSEEUG00000001116	1 retrocopy	retro_eeur_377 ,
Monodelphis domestica	ENSMODG00000009685	2 retrocopies	retro_mdom_1002, retro_mdom_572,
Mus musculus	ENSMUSG00000031226	1 retrocopy	retro_mmus_1569,
Oryctolagus cuniculus	ENSOCUG00000001088	3 retrocopies	retro_ocun_1017, retro_ocun_1402, retro_ocun_595,
Otolemur garnettii	ENSOGAG00000015205	1 retrocopy	retro_ogar_3063,
Rattus norvegicus	ENSRNOG00000002662	3 retrocopies	retro_rnor_1703, retro_rnor_1705, retro_rnor_826,
Sarcophilus harrisii	ENSSHAG00000017872	1 retrocopy	retro_shar_132,
Tupaia belangeri	ENSTBEG00000003411	3 retrocopies	retro_tbel_3448, retro_tbel_494, retro_tbel_979,