RetrogeneDB ID: retro_eeur_553

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_343346:37136..37531(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL6
• Ensembl ID: ENSEEUG00000000281
• Aliases: None
• Description: ribosomal protein L6 [Source:HGNC Symbol;Acc:10362]

Sequence

>retro_eeur_553
CACAGAGGCAAAAGGGTGGTTTTTCTTGAAGCAGCTGGACATGGCTTATTCCTTGTGACTAAACCTCTGTCACTCAACCG
AGTTCCTCTGCATAGAACACACCAGAAATTTGTCATTGCCACCTCCACCAAAATTGATATCAGTGGTGTGAAAATCCCCA
ACCATCTCACTGATACTTACTTCAACAAGAAGAAGAAACTGCAAAAGCCCAGACACCAGGAAATGAGTTCTCTGACACGG
AAAAGAAAGGCAAGATTACAGAGCAGTACAACGTTGATCAGAAAGCTCTGCACTCACAGATCTTGCTGAAAATTAAAGCC
ATTCCTCAACTCCAGGGCTATCTCTGCCCTGTGTTTGCTCTCACAAATGGACTTTACCTGCATAAAGTGGTGTTC

Alignment

ORF - retro_eeur_553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.87 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HRGKRVVFLKQLESGLLLVTGPLSLNRVPLRRTHQKFVIATSTKIDISSVKIPKHLTDTYF-KKKKLRKP
          HRGKRVVFL.....GL.LVT.PLSLNRVPL.RTHQKFVIATSTKIDIS.VKIP.HLTDTYF.KKKKL.KP
Retrocopy HRGKRVVFLEAAGHGLFLVTKPLSLNRVPLHRTHQKFVIATSTKIDISGVKIPNHLTDTYFNKKKKLQKP

Parental  RHQE-GEIFDTEKEKYEITEQRKVDQKAVDSQILPRIKAVPQLQGYLRSVFALTNGIYPHKLVF
          RHQE..E..DTEK.K..ITEQ..VDQKA..SQIL..IKA.PQLQGYL..VFALTNG.Y.HK.VF
Retrocopy RHQE<NEFSDTEK-KGKITEQYNVDQKALHSQILLKIKAIPQLQGYLCPVFALTNGLYLHKVVF

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	203.04 RPM
SRP017611_kidney	0.00 RPM	458.53 RPM
SRP017611_liver	0.00 RPM	321.55 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_553 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 23 parental genes, and 182 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003060	1 retrocopy	retro_acar_171,
Bos taurus	ENSBTAG00000031723	6 retrocopies	retro_btau_1038, retro_btau_1117, retro_btau_1305, retro_btau_16, retro_btau_424, retro_btau_809,
Canis familiaris	ENSCAFG00000008873	1 retrocopy	retro_cfam_36,
Callithrix jacchus	ENSCJAG00000012450	7 retrocopies	retro_cjac_1362, retro_cjac_1620, retro_cjac_1949, retro_cjac_2723, retro_cjac_328, retro_cjac_349, retro_cjac_497,
Cavia porcellus	ENSCPOG00000013526	8 retrocopies	retro_cpor_1105, retro_cpor_1149, retro_cpor_1486, retro_cpor_382, retro_cpor_412, retro_cpor_651, retro_cpor_731, retro_cpor_982,
Dipodomys ordii	ENSDORG00000005793	1 retrocopy	retro_dord_166,
Equus caballus	ENSECAG00000017514	1 retrocopy	retro_ecab_811,
Erinaceus europaeus	ENSEEUG00000000281	3 retrocopies	retro_eeur_503, retro_eeur_553 , retro_eeur_595,
Felis catus	ENSFCAG00000006858	12 retrocopies	retro_fcat_1264, retro_fcat_1370, retro_fcat_1844, retro_fcat_232, retro_fcat_398, retro_fcat_500, retro_fcat_625, retro_fcat_637, retro_fcat_643, retro_fcat_690, retro_fcat_926, retro_fcat_935,
Homo sapiens	ENSG00000089009	26 retrocopies	retro_hsap_1035, retro_hsap_146, retro_hsap_1905, retro_hsap_2074, retro_hsap_2164, retro_hsap_2206, retro_hsap_227, retro_hsap_2566, retro_hsap_2720, retro_hsap_2725, retro_hsap_2939, retro_hsap_2955, retro_hsap_3009, retro_hsap_3014, retro_hsap_3070, retro_hsap_333, retro_hsap_3431, retro_hsap_3559, retro_hsap_3795, retro_hsap_3818, retro_hsap_3856, retro_hsap_4039, retro_hsap_440, retro_hsap_4729, retro_hsap_4788, retro_hsap_648,
Gorilla gorilla	ENSGGOG00000003372	16 retrocopies	retro_ggor_1602, retro_ggor_1893, retro_ggor_1898, retro_ggor_2047, retro_ggor_2138, retro_ggor_236, retro_ggor_2569, retro_ggor_2597, retro_ggor_2709, retro_ggor_2745, retro_ggor_290, retro_ggor_2938, retro_ggor_356, retro_ggor_426, retro_ggor_566, retro_ggor_816,
Microcebus murinus	ENSMICG00000002961	25 retrocopies	retro_mmur_1053, retro_mmur_1068, retro_mmur_1105, retro_mmur_1133, retro_mmur_1134, retro_mmur_1174, retro_mmur_1212, retro_mmur_1248, retro_mmur_1311, retro_mmur_1512, retro_mmur_1564, retro_mmur_190, retro_mmur_200, retro_mmur_201, retro_mmur_208, retro_mmur_324, retro_mmur_356, retro_mmur_361, retro_mmur_497, retro_mmur_613, retro_mmur_616, retro_mmur_716, retro_mmur_814, retro_mmur_848, retro_mmur_921,
Macaca mulatta	ENSMMUG00000007433	1 retrocopy	retro_mmul_171,
Monodelphis domestica	ENSMODG00000003096	4 retrocopies	retro_mdom_1556, retro_mdom_1624, retro_mdom_1784, retro_mdom_615,
Mustela putorius furo	ENSMPUG00000002526	9 retrocopies	retro_mputfur_1116, retro_mputfur_1279, retro_mputfur_1320, retro_mputfur_1367, retro_mputfur_1407, retro_mputfur_1445, retro_mputfur_1489, retro_mputfur_401, retro_mputfur_571,
Mus musculus	ENSMUSG00000029614	13 retrocopies	retro_mmus_1264, retro_mmus_1336, retro_mmus_1898, retro_mmus_2684, retro_mmus_276, retro_mmus_3065, retro_mmus_3579, retro_mmus_3611, retro_mmus_3622, retro_mmus_3719, retro_mmus_445, retro_mmus_465, retro_mmus_730,
Nomascus leucogenys	ENSNLEG00000027093	2 retrocopies	retro_nleu_1813, retro_nleu_43,
Oryctolagus cuniculus	ENSOCUG00000003802	5 retrocopies	retro_ocun_129, retro_ocun_17, retro_ocun_189, retro_ocun_229, retro_ocun_245,
Pongo abelii	ENSPPYG00000025855	13 retrocopies	retro_pabe_1764, retro_pabe_1891, retro_pabe_2451, retro_pabe_2493, retro_pabe_2573, retro_pabe_2897, retro_pabe_3314, retro_pabe_358, retro_pabe_3677, retro_pabe_3725, retro_pabe_43, retro_pabe_472, retro_pabe_868,
Rattus norvegicus	ENSRNOG00000025936	1 retrocopy	retro_rnor_129,
Sarcophilus harrisii	ENSSHAG00000007096	2 retrocopies	retro_shar_506, retro_shar_536,
Ictidomys tridecemlineatus	ENSSTOG00000009409	3 retrocopies	retro_itri_1024, retro_itri_1125, retro_itri_684,
Tarsius syrichta	ENSTSYG00000009492	22 retrocopies	retro_tsyr_1046, retro_tsyr_1254, retro_tsyr_1600, retro_tsyr_1615, retro_tsyr_2052, retro_tsyr_2080, retro_tsyr_2123, retro_tsyr_2126, retro_tsyr_291, retro_tsyr_362, retro_tsyr_364, retro_tsyr_438, retro_tsyr_477, retro_tsyr_490, retro_tsyr_566, retro_tsyr_586, retro_tsyr_626, retro_tsyr_637, retro_tsyr_774, retro_tsyr_833, retro_tsyr_894, retro_tsyr_923,