RetrogeneDB ID: retro_eeur_223

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_213319:10067..10585(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSEEUG00000012238
• Aliases: None
• Description: high mobility group box 2 [Source:HGNC Symbol;Acc:5000]

Sequence

>retro_eeur_223
ATGGGCAAAGGAGATCCTAAGAAGCCAAGAGGCGAAACATCATCATATGCATTCTTTGTGCAAACTTGCTGCGAGGAGCA
CAAGAAGAAGTACCCAGATGTTTCAGTCAACTTTTCAGAATTTTCTAAGAAGTGCCCAGATAGTTAGAAGACCATGTCTG
CTAAAGAGAAAGGAACATTTTAAGGCATGGCAAAGGCTGACAAGGCCCATTATGAAAGAGAAATGAAACTTATATCCCCC
CTAAAGGGGAAACAAAAAAGAAATTCAAGGACCCCAATGTACCTAAGAAGCCTCTGTCGGCCTTTTTCTTGTTTTGTTCT
GAGTATCAACCCAAAATCAAAGGAGAACATCCTGGCCTATCCATTGGTGATGCTGCAAAGAAACTGGGAGAGACGTGGAA
TAACACTGCCGCAGATGACAAGCAGCCTTATGGGAAGAAGGCTGCTAAGATGAAGGAAAAATACGAAAAGGATATTGCTG
CCTACCGAGCTAAAGGCAAGCCTGATACAGCCACAAAG

Alignment

ORF - retro_eeur_223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 84.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKAR
          MGKGDP.KPRG..SSYAFFVQTC.EEHKKK.PD.SVNF.EFSKKC....KTMSAKEK..F..MAK.DKA.
Retrocopy MGKGDPKKPRGETSSYAFFVQTCCEEHKKKYPDVSVNFSEFSKKCPDS*KTMSAKEKGTF*GMAKADKAH

Parental  YDREMK-NYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSKHHPKIKSEHPGLSHWDTAKKLGEMWSEQSAK
          Y.REMK..Y.PPKG..K.K.KDPN.PK.P.SAFFLFCS...PKIK.EHPGLS..D.AKKLGE.W....A.
Retrocopy YEREMK<TYIPPKGETKKKFKDPNVPKKPLSAFFLFCSEYQPKIKGEHPGLSIGDAAKKLGETWNNTAAD

Parental  DKQPYEQTAANLTEKCEKDIASYRAKGKSEAGKR
          DKQPY...AA...EK.EKDIA.YRAKGK......
Retrocopy DKQPYGKKAAKMKEKYEKDIAAYRAKGKPDTATK

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	1.93 RPM	2.26 RPM
SRP017611_kidney	2.06 RPM	3.56 RPM
SRP017611_liver	0.80 RPM	3.70 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_223 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 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015101	1 retrocopy	retro_btau_58,
Cavia porcellus	ENSCPOG00000003552	4 retrocopies	retro_cpor_1100, retro_cpor_604, retro_cpor_890, retro_cpor_980,
Dasypus novemcinctus	ENSDNOG00000019440	4 retrocopies	retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
Erinaceus europaeus	ENSEEUG00000012238	8 retrocopies	retro_eeur_118, retro_eeur_223 , retro_eeur_345, retro_eeur_49, retro_eeur_54, retro_eeur_661, retro_eeur_702, retro_eeur_86,
Echinops telfairi	ENSETEG00000010379	3 retrocopies	retro_etel_1474, retro_etel_1841, retro_etel_2023,
Echinops telfairi	ENSETEG00000016379	1 retrocopy	retro_etel_414,
Felis catus	ENSFCAG00000004218	2 retrocopies	retro_fcat_279, retro_fcat_52,
Homo sapiens	ENSG00000164104	1 retrocopy	retro_hsap_3663,
Gorilla gorilla	ENSGGOG00000015882	1 retrocopy	retro_ggor_2474,
Macropus eugenii	ENSMEUG00000002256	3 retrocopies	retro_meug_1920, retro_meug_1989, retro_meug_550,
Monodelphis domestica	ENSMODG00000003527	3 retrocopies	retro_mdom_1160, retro_mdom_1919, retro_mdom_69,
Nomascus leucogenys	ENSNLEG00000006662	3 retrocopies	retro_nleu_113, retro_nleu_517, retro_nleu_550,
Pongo abelii	ENSPPYG00000015204	3 retrocopies	retro_pabe_297, retro_pabe_3005, retro_pabe_3380,
Pan troglodytes	ENSPTRG00000016597	3 retrocopies	retro_ptro_19, retro_ptro_2484, retro_ptro_2789,
Rattus norvegicus	ENSRNOG00000013167	2 retrocopies	retro_rnor_173, retro_rnor_54,
Tursiops truncatus	ENSTTRG00000015650	1 retrocopy	retro_ttru_1640,