RetrogeneDB ID: retro_eeur_439

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_303409:48835..49477(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: S100PBP
• Ensembl ID: ENSEEUG00000006053
• Aliases: None
• Description: S100P binding protein [Source:HGNC Symbol;Acc:25768]

Sequence

>retro_eeur_439
GAAAGTAAGATAACAGAAGATGGTCTTAGCCCAAATGAGACCAACCTTTGCACTGAATCTGAAGGAACTGGCCCTAGTAA
CTCTGCCCAAAAGGGGTCTCATTTCCCTTTTCCTTCAAACAGTAAGAAAACTGTCTCTGTAGTCTCTCAAACCTTGGACC
ACTCAGAAACTCCCCAAGAAGTCCAGTCATCATGGAAAAATGGATCACATAAATCAAGTGAAATGAGTTCTCCAGTTATT
TCCACTTCATCAGACAAAAGGCAGGGTGCTCTTGGCAAGGATTCTGGGAAGCTAAAAATCCAAGAGAGAAGACTAGGTAA
AGTCATTCCTGTTCTACAAACCCAAACCAGGACTCATGCTCCTCAAGCAGATCTAGAAGCAGAGAAGCAAAGGTATCTCA
GTAATGTCATTGCTCACTTAGAAGGCTCAGAGGATGCTAACCAAGGTACTTGGGGGGAGCTCTATGCCTTAATGGATCAA
GTTCATCATACGCATACCCCAAAGTGGCAGCATCCTTCAGACCTTACTAAACGAAACTATGCCCGGTTCCGACAGAATTC
CCGGCAAAAATACAGTCTGACTCAGTGGGTTGATAGAAATGAACGAAGCCACCATCGATTCCAACGGCTCCCATGCACTC
CT

Alignment

ORF - retro_eeur_439 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.52 %
• Parental protein coverage: 54.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESKITEDGLSPNETNLCTESEGTGPSNSAQKGSHFPF-LQSKKTVSVVSQTLDHSETPQEVQSSWKNGSH
          ESKITEDGLSPNETNLCTESEGTGPSNSAQKGSHFPF...SKKTVSVVSQTLDHSETPQEVQSSWKNGSH
Retrocopy ESKITEDGLSPNETNLCTESEGTGPSNSAQKGSHFPFPSNSKKTVSVVSQTLDHSETPQEVQSSWKNGSH

Parental  KSSEMSSPVISTSSDK-QGALGKDSEKLKIQERRLGKVIPVLQTQT-THAPQADLEAEKQRYLSNVIAHL
          KSSEMSSPVISTSSDK.QGALGKDS.KLKIQERRLGKVIPVLQTQT.THAPQADLEAEKQRYLSNVIAHL
Retrocopy KSSEMSSPVISTSSDKRQGALGKDSGKLKIQERRLGKVIPVLQTQTRTHAPQADLEAEKQRYLSNVIAHL

Parental  EGSEDVNQGTWGELCALMDQVLHTHTPKWQHPSDLTKRNCAQF-QNSQQRYSLTQWVDRNE-SHHRFQWL
          EGSED.NQGTWGEL.ALMDQV.HTHTPKWQHPSDLTKRN.A.F.QNS.Q.YSLTQWVDRNE.SHHRFQ.L
Retrocopy EGSEDANQGTWGELYALMDQVHHTHTPKWQHPSDLTKRNYARFRQNSRQKYSLTQWVDRNERSHHRFQRL

Parental  PCTP
          PCTP
Retrocopy PCTP

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	14.02 RPM	12.09 RPM
SRP017611_kidney	15.94 RPM	8.81 RPM
SRP017611_liver	2.25 RPM	1.77 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_439 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000537	1 retrocopy	retro_dnov_1346,
Erinaceus europaeus	ENSEEUG00000006053	1 retrocopy	retro_eeur_439 ,
Myotis lucifugus	ENSMLUG00000000764	1 retrocopy	retro_mluc_1691,
Monodelphis domestica	ENSMODG00000017396	2 retrocopies	retro_mdom_1633, retro_mdom_62,
Tursiops truncatus	ENSTTRG00000014993	1 retrocopy	retro_ttru_89,