RetrogeneDB ID: retro_eeur_354

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_268473:298..867(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000000339
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000010307
• Aliases: None
• Description: None

Sequence

>retro_eeur_354
AAGAAGTTTGCCCAGAAGATGCTTCAGAAGGCAAGAAGGAAGCTTAGCTATGCAAAAGTTAAGCACCATAATAAGGAATA
TAGTCAAATATACTGAACCAAGATTCGAATGGCTAGGATGACAAGAAAATCTGGCAACTTCCATGTATCTGCAGAACCTA
ATCTGGCATTCGTTATCAGGATCAGAGGTAGCAATGGTGTGAGCCCAAAGGTCTGAAAGGTGTTGCAACTTCTTCGCCTT
TGACAGATGTTTAGTGGCACCTTTGTTAAGCTCAATAGGCTTCAGTTAACATGCTGAGAATTGTGGAACCCTATATTGCT
TGGGGGTACCCAAATCTGACGTTAGTAAATGAACTGATCTACAAGTGAGTTTATGGCAAAATTCACAAGAGACAGATTGC
TCTGACTGGTAAGTCCTTGACTGCTCGATCCCTTGGTAAATATGGCATCATCTGCATGGAGGATCTGATTCATGAGAGCT
ACACTGTTGGAAAACACTTCAAAAAAGCAAACAACTTCCTCTGGCCAATCAAATTATCTTCTCCACAAGGTGGTATGAGG
AAAAAGACC

Alignment

ORF - retro_eeur_354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.1 %
• Parental protein coverage: 76.61 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKFAQKMLRKARRKLIYEKAKYYHKEYSQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPK
          KKFAQKML.KARRKL.Y.K.K...KEYSQ.Y.T.IRMARM.RK.GNF.V.AEP.LAFVIRIRG.NGVSPK
Retrocopy KKFAQKMLQKARRKLSYAKVKHHNKEYSQIY*TKIRMARMTRKSGNFHVSAEPNLAFVIRIRGSNGVSPK

Parental  VRKVLQLLRLRQIFNGTFVKLNK-ASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKIHKKRIALTDNS
          V.KVLQLLRL.Q.F.GTFVKLN..AS.NMLRIVEPYIAWGYPNL..VNELIYK..YGKIHK..IALT..S
Retrocopy V*KVLQLLRL*QMFSGTFVKLNR<ASVNMLRIVEPYIAWGYPNLTLVNELIYK*VYGKIHKRQIALTGKS

Parental  LIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKT
          L.ARSLGKYGIICMEDLIHE.YTVGK.FK.ANNFLWP.KLSSP.GGM.KKT
Retrocopy LTARSLGKYGIICMEDLIHESYTVGKHFKKANNFLWPIKLSSPQGGMRKKT

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	294.73 RPM
SRP017611_kidney	0.19 RPM	720.71 RPM
SRP017611_liver	0.00 RPM	434.09 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_354 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 10 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004140	18 retrocopies	retro_cpor_1056, retro_cpor_1190, retro_cpor_1342, retro_cpor_1347, retro_cpor_1348, retro_cpor_1366, retro_cpor_1418, retro_cpor_1449, retro_cpor_1452, retro_cpor_1453, retro_cpor_187, retro_cpor_209, retro_cpor_245, retro_cpor_266, retro_cpor_397, retro_cpor_458, retro_cpor_506, retro_cpor_640,
Erinaceus europaeus	ENSEEUG00000010307	3 retrocopies	retro_eeur_354 , retro_eeur_420, retro_eeur_55,
Erinaceus europaeus	ENSEEUG00000010431	1 retrocopy	retro_eeur_90,
Echinops telfairi	ENSETEG00000005656	33 retrocopies	retro_etel_1099, retro_etel_1120, retro_etel_1154, retro_etel_1158, retro_etel_1333, retro_etel_1370, retro_etel_1553, retro_etel_1642, retro_etel_1708, retro_etel_1720, retro_etel_175, retro_etel_185, retro_etel_1891, retro_etel_2042, retro_etel_2044, retro_etel_2118, retro_etel_2149, retro_etel_265, retro_etel_316, retro_etel_375, retro_etel_402, retro_etel_519, retro_etel_532, retro_etel_554, retro_etel_610, retro_etel_793, retro_etel_865, retro_etel_869, retro_etel_877, retro_etel_887, retro_etel_889, retro_etel_992, retro_etel_993,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Mustela putorius furo	ENSMPUG00000010240	15 retrocopies	retro_mputfur_1004, retro_mputfur_1031, retro_mputfur_1034, retro_mputfur_1035, retro_mputfur_1156, retro_mputfur_1168, retro_mputfur_1384, retro_mputfur_1454, retro_mputfur_1481, retro_mputfur_390, retro_mputfur_410, retro_mputfur_545, retro_mputfur_839, retro_mputfur_929, retro_mputfur_982,
Nomascus leucogenys	ENSNLEG00000026615	8 retrocopies	retro_nleu_1012, retro_nleu_1459, retro_nleu_1696, retro_nleu_1853, retro_nleu_2479, retro_nleu_2603, retro_nleu_3, retro_nleu_901,
Sorex araneus	ENSSARG00000001088	3 retrocopies	retro_sara_268, retro_sara_310, retro_sara_623,