RetrogeneDB ID: retro_eeur_197

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_206520:283..808(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCTS1
• Ensembl ID: ENSEEUG00000007258
• Aliases: None
• Description: malignant T cell amplified sequence 1 [Source:HGNC Symbol;Acc:23357]

Sequence

>retro_eeur_197
AAGTTCGACGAGAAGGAGGACGTGTCTCACTGCGTGCAGCTGAAGACGTCGGTGATCAAGGGCATCCGCAGCCAGCTGGC
CGCTCAGTTCCCGGGCGCCGCGCCCTGGCTGGGCCGCATCCTGCCGCGCCGCGAGCCCGTCCGCCTGCTGCGCTGTCACG
AGCACGTGGAGATCCTGGCGGCGGGCGGCGAGCTGCTCTTCTTTCGCCGGCGCGACGGGCCCTTCTACCCGACGCTGCGC
CTGCTGCACAAGTTCCCGTGCCTGCTGCCGCAGCAGCAGGTGGACAAGGGCGCCATCAAGTTCGTGCTGAGCGGCGCGCA
CGTCATGTGCCCCGGCCTGACCTCGCCCGGCGCCCGCCTGCTGCCCGCCGCGGCCGACACGGTGGTGGCGCTCATGGCCG
AGGGCAAGCGGCACGCGCTGTGCGTGGGCGTCATGAAGATGTCGGCCGACGACATCGAGCGCGTCAACAGGGGCGTGGGC
ATCGAGAACGTGCACCACCTCAACGACGGGCTGTGGCACATGAAG

Alignment

ORF - retro_eeur_197 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.0 %
• Parental protein coverage: 96.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLFFRQ
          .FDEKE.VS.C.QLKTSVIKGI..QL..QFPG..PWL..I.P...PV...RCHEH.EIL...GELLFFR.
Retrocopy KFDEKEDVSHCVQLKTSVIKGIRSQLAAQFPGAAPWLGRILPRREPVRLLRCHEHVEILAAGGELLFFRR

Parental  REGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTVVAIMAEGKQHAL
          R.GPFYPTLRLLHK.P..LP.QQVDKGAIKFVLSGA..MCPGLTSPGA.L.PAA.DTVVA.MAEGK.HAL
Retrocopy RDGPFYPTLRLLHKFPCLLPQQQVDKGAIKFVLSGAHVMCPGLTSPGARLLPAAADTVVALMAEGKRHAL

Parental  CVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMK
          CVGVMKMSA.DIE.VN.G.GIEN.H.LNDGLWHMK
Retrocopy CVGVMKMSADDIERVNRGVGIENVHHLNDGLWHMK

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	0.00 RPM	40.29 RPM
SRP017611_kidney	0.00 RPM	49.32 RPM
SRP017611_liver	0.00 RPM	34.89 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_197 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 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411,
Erinaceus europaeus	ENSEEUG00000007258	1 retrocopy	retro_eeur_197 ,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Homo sapiens	ENSG00000232119	1 retrocopy	retro_hsap_2422,
Gorilla gorilla	ENSGGOG00000009420	1 retrocopy	retro_ggor_1507,
Myotis lucifugus	ENSMLUG00000015101	1 retrocopy	retro_mluc_16,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Pan troglodytes	ENSPTRG00000022241	1 retrocopy	retro_ptro_1396,
Pteropus vampyrus	ENSPVAG00000013249	3 retrocopies	retro_pvam_1323, retro_pvam_645, retro_pvam_867,
Rattus norvegicus	ENSRNOG00000002563	2 retrocopies	retro_rnor_1841, retro_rnor_957,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,
Tupaia belangeri	ENSTBEG00000010666	2 retrocopies	retro_tbel_1485, retro_tbel_4265,
Tarsius syrichta	ENSTSYG00000001440	1 retrocopy	retro_tsyr_55,
Tursiops truncatus	ENSTTRG00000007208	1 retrocopy	retro_ttru_1587,