RetrogeneDB ID: retro_eeur_240

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_219522:805..1287(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL5A
• Ensembl ID: ENSEEUG00000009350
• Aliases: None
• Description: ADP-ribosylation factor-like 5A [Source:HGNC Symbol;Acc:696]

Sequence

>retro_eeur_240
CACAAAGTTATCATTGTTGGCTGGATAACGCAGAGAAAACTACCATCCTTTACCAGTTTTCTATGAATGAAGTTGTACAC
ACATCCCCCAAAACAGGAAGTAATGTAGAGGAGATAGTGGTTAATAATACACATTTCCTAATGTGGGATCTTGGTGGCCA
AGAATCTCTTCGTTCTTCCTGGAACACTTACTATACTAACACAGAGTTTGTAATCATTGTTGTAGATAGTTCGGACAGAG
AAAGAATTTCTGTAACTAGAGAAAAACTCTATAAAATGTTAGCCCATGAGGACCTAAGGAAAGCCGGATTACTGATTTTT
ACTAATAAGCAAGACGTTAAGGAATGCATGACTGTAGCAGAGATCTCCCAGTTTTTAAAGCTGACATCTATTAAAAACCA
CCAACGGCATATACAGGCATGCTGTGCTCTTACTGGTGAAGGATTATGCCAAGGACTTGAGTGGATGATGTCACGGCTGA
AG

Alignment

ORF - retro_eeur_240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.51 %
• Parental protein coverage: 98.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HKVIIVG-LDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVVNNTRFLMWDIGGQESLRSSWNTYYTNTE
          HKVIIVG.LDNA.KTTILYQFSMNEVVHTSP..GSNVEEIVVNNT.FLMWD.GGQESLRSSWNTYYTNTE
Retrocopy HKVIIVG<LDNAEKTTILYQFSMNEVVHTSPKTGSNVEEIVVNNTHFLMWDLGGQESLRSSWNTYYTNTE

Parental  FVIIVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQ
          FVIIVVDS.DRERISVTRE.LYKMLAHEDLRKAGLLIF.NKQDVKECMTVAEISQFLKLTSIK.HQ.HIQ
Retrocopy FVIIVVDSSDRERISVTREKLYKMLAHEDLRKAGLLIFTNKQDVKECMTVAEISQFLKLTSIKNHQRHIQ

Parental  ACCALTGEGVCEGLGGMMARLE
          ACCALTGEG.C.GL..MM.RL.
Retrocopy ACCALTGEGLCQGLEWMMSRLK

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	1.61 RPM	11.28 RPM
SRP017611_kidney	3.38 RPM	16.13 RPM
SRP017611_liver	6.11 RPM	19.45 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_240 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 15 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005062	25 retrocopies	retro_chof_1109, retro_chof_1132, retro_chof_1205, retro_chof_1218, retro_chof_1407, retro_chof_1414, retro_chof_1443, retro_chof_1573, retro_chof_1712, retro_chof_1953, retro_chof_206, retro_chof_2081, retro_chof_2131, retro_chof_2142, retro_chof_2433, retro_chof_2464, retro_chof_2470, retro_chof_2713, retro_chof_373, retro_chof_547, retro_chof_836, retro_chof_857, retro_chof_865, retro_chof_972, retro_chof_98,
Callithrix jacchus	ENSCJAG00000003311	9 retrocopies	retro_cjac_1054, retro_cjac_1111, retro_cjac_1255, retro_cjac_1921, retro_cjac_2949, retro_cjac_3920, retro_cjac_4131, retro_cjac_4175, retro_cjac_4211,
Dasypus novemcinctus	ENSDNOG00000013331	16 retrocopies	retro_dnov_105, retro_dnov_1165, retro_dnov_1244, retro_dnov_1953, retro_dnov_2159, retro_dnov_226, retro_dnov_2265, retro_dnov_2268, retro_dnov_2344, retro_dnov_2394, retro_dnov_563, retro_dnov_671, retro_dnov_713, retro_dnov_811, retro_dnov_818, retro_dnov_881,
Equus caballus	ENSECAG00000023672	1 retrocopy	retro_ecab_1087,
Erinaceus europaeus	ENSEEUG00000009350	3 retrocopies	retro_eeur_240 , retro_eeur_642, retro_eeur_699,
Felis catus	ENSFCAG00000014742	2 retrocopies	retro_fcat_569, retro_fcat_65,
Gorilla gorilla	ENSGGOG00000002066	5 retrocopies	retro_ggor_1131, retro_ggor_1594, retro_ggor_2930, retro_ggor_2971, retro_ggor_3056,
Loxodonta africana	ENSLAFG00000032104	4 retrocopies	retro_lafr_1178, retro_lafr_1228, retro_lafr_1244, retro_lafr_599,
Monodelphis domestica	ENSMODG00000003978	1 retrocopy	retro_mdom_75,
Mustela putorius furo	ENSMPUG00000000396	2 retrocopies	retro_mputfur_1477, retro_mputfur_352,
Mus musculus	ENSMUSG00000036093	1 retrocopy	retro_mmus_2232,
Ictidomys tridecemlineatus	ENSSTOG00000016326	1 retrocopy	retro_itri_62,
Tupaia belangeri	ENSTBEG00000011511	8 retrocopies	retro_tbel_1173, retro_tbel_1540, retro_tbel_3202, retro_tbel_3464, retro_tbel_3681, retro_tbel_3835, retro_tbel_4207, retro_tbel_4665,
Tursiops truncatus	ENSTTRG00000015564	2 retrocopies	retro_ttru_1008, retro_ttru_1843,
Vicugna pacos	ENSVPAG00000002172	2 retrocopies	retro_vpac_318, retro_vpac_399,