RetrogeneDB ID: retro_eeur_311

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_250517:3741..4245(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000006203
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000006985
• Aliases: None
• Description: None

Sequence

>retro_eeur_311
CAAAAAGCAAAGACCAAGACCACCAAGAAGTGCCCCCAACGTGCGACATCCAACGTCTTTGCCATGTTTGACCAGTCTCA
GATTCAGGAGTTCAAAGAGGAATTCAACATGATCGATCAGAACAGAGATAACGTCATTGACAAGGAAGACTTGCAGGGCA
TGCTTGCTTCCCTAGGGAAGAATCCCACTGATACATACCATGACGCCATGATGAATGAGGCCCCAGACCCCATCAGTTTC
ACCATGTTCCTCACAATGTTTGAGGAAACATTAAATGGTACAGATCCTGAAGATATCAGAAATGCCTTTGCCTGCTTTGA
TGAAGAAGCAACTGGCACCATCCAGGAAGACTACCTGAGGGAGCCTCCTGCTGACAATAGGGGACTGCTTCACAGAAGAG
GGGGTGGATGAACTGTACCGGGGAGTGTTTATAGACAAAAGGGCAATTACAACTACATTGAGTTCACGTGCATCCTTAAA
CATGGCGCCAAAGACAAGAATGAC

Alignment

ORF - retro_eeur_311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 98.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDAYLDAM
          .KAKTKTTKK.PQRATSNVFAMFDQSQIQEFKE.FNMIDQNRD..IDKEDL..MLASLGKNPTD.Y.DAM
Retrocopy QKAKTKTTKKCPQRATSNVFAMFDQSQIQEFKEEFNMIDQNRDNVIDKEDLQGMLASLGKNPTDTYHDAM

Parental  MNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRE-LLTTMGDRFTDEEVDEL
          MNEAP.PI.FTMFLTMF.E.LNGTDPED.IRNAFACFDEEATGTIQEDYLRE.LL.T.GD.FT.E.VDEL
Retrocopy MNEAPDPISFTMFLTMFEETLNGTDPED-IRNAFACFDEEATGTIQEDYLRE>LLLTIGDCFTEEGVDEL

Parental  YREAPIDK-KGNFNYIEFTRILKHGAKDKDD
          YR...IDK.KGN.NYIEFT.ILKHGAKDK.D
Retrocopy YRGVFIDK<KGNYNYIEFTCILKHGAKDKND

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	0.16 RPM	23.69 RPM
SRP017611_kidney	0.56 RPM	205.73 RPM
SRP017611_liver	0.00 RPM	27.49 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_311 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 21 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012665	1 retrocopy	retro_amel_1847,
Canis familiaris	ENSCAFG00000032168	1 retrocopy	retro_cfam_1224,
Dasypus novemcinctus	ENSDNOG00000007004	2 retrocopies	retro_dnov_463, retro_dnov_953,
Dipodomys ordii	ENSDORG00000007562	1 retrocopy	retro_dord_531,
Erinaceus europaeus	ENSEEUG00000006985	1 retrocopy	retro_eeur_311 ,
Felis catus	ENSFCAG00000022871	1 retrocopy	retro_fcat_2019,
Homo sapiens	ENSG00000118680	4 retrocopies	retro_hsap_1487, retro_hsap_3129, retro_hsap_3451, retro_hsap_3985,
Gorilla gorilla	ENSGGOG00000004051	4 retrocopies	retro_ggor_1139, retro_ggor_1140, retro_ggor_2330, retro_ggor_2675,
Myotis lucifugus	ENSMLUG00000005189	2 retrocopies	retro_mluc_706, retro_mluc_947,
Monodelphis domestica	ENSMODG00000021464	1 retrocopy	retro_mdom_987,
Mustela putorius furo	ENSMPUG00000005011	1 retrocopy	retro_mputfur_294,
Mus musculus	ENSMUSG00000034868	2 retrocopies	retro_mmus_1483, retro_mmus_1539,
Nomascus leucogenys	ENSNLEG00000006907	3 retrocopies	retro_nleu_1709, retro_nleu_1906, retro_nleu_2250,
Oryctolagus cuniculus	ENSOCUG00000021304	1 retrocopy	retro_ocun_900,
Otolemur garnettii	ENSOGAG00000029777	2 retrocopies	retro_ogar_2409, retro_ogar_857,
Ochotona princeps	ENSOPRG00000009826	2 retrocopies	retro_opri_342, retro_opri_736,
Pongo abelii	ENSPPYG00000009032	3 retrocopies	retro_pabe_1236, retro_pabe_2585, retro_pabe_3026,
Pan troglodytes	ENSPTRG00000009836	4 retrocopies	retro_ptro_1006, retro_ptro_2118, retro_ptro_2340, retro_ptro_2705,
Rattus norvegicus	ENSRNOG00000015733	2 retrocopies	retro_rnor_1614, retro_rnor_2718,
Tupaia belangeri	ENSTBEG00000009299	4 retrocopies	retro_tbel_1294, retro_tbel_1629, retro_tbel_3088, retro_tbel_3438,
Tarsius syrichta	ENSTSYG00000010418	9 retrocopies	retro_tsyr_1034, retro_tsyr_1265, retro_tsyr_1320, retro_tsyr_1464, retro_tsyr_1961, retro_tsyr_2054, retro_tsyr_277, retro_tsyr_391, retro_tsyr_751,