RetrogeneDB ID: retro_eeur_482

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_322592:5520..6378(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA2
• Ensembl ID: ENSEEUG00000009063
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 2 [Source:HGNC Symbol;Acc:1490]

Sequence

>retro_eeur_482
ATGGCCGACTTCGAGCATTGCGTGTCGGATGACGAGAAGGTAGCATAGCTGCTAAATCCGCTCCCCCACCTCCCCGAGGG
GAATTTAATGAAGTATTCAACGATGTCCGGCTGCTACTTAATAATGACAATCTCCTCAGGGAAAGGAGCAGCGCATGCAT
TTGCCCAGTATAACATGGATCAGCTCACACCAGTGAAGATAGAAGGATATGAAGAACAGGTCTTAATTACAGAACATGGT
GACCTGGGCAATAGCAGATTTTTAGATCCAAAAAACAAAATTTCCTTTAAATTTGATCATTTACCGAAAGAAGCAAGTGA
CCCTCATCCAGAAGAAGCAGATGGAGGTCTGAAATCTTGGAGAGAATCCTATGACAGTGCTTTAAGGGCCTATGTGAAAG
ACCATTATTCCCACGGCTTCTGTACTGTTTATGCTAAAACTATAGATGGACAGCAGACCATTATTGCATGTATTGAAAGT
CACCAGTTTCAGCCTCAGAACTTCTGGAATGGTCGTTGGAGATCACAGTGGAAGTTCACCATCACACCACCTACAGCTCA
AGTGGTTGGAGTACTTAAGATTCAGGTTCACTATTATGAAGACGGCAATGTTCAGTTGTCTAGTCATAAAGACGTACGGG
ATTCAGTAACTGTTTCAAATTAAGTCCCAACTGCCAAGGAGTTTATTAAAATCATAGAGCATGCAGAAAATGAGTATCAG
ACAGCAATTAGTGAAAACTATCAAACAATGTCAGACACCACATTCAAGGCCTTGCACTGGCAGCTTCCAGTTACCCACAC
CAAAATCGACTGGAACAAGATACTCAGCTACAAGATTGGCAAAGAAATGCAGAATGCT

Alignment

ORF - retro_eeur_482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADLEEQLSDEEKVR-IAAKFIIHAPPGEFNEVFNDVRLLLNNDNLLRE-GAAQALAQYNLD--TPVKIE
          MAD.E...SD.EKV..IAAK.....P.GEFNEVFNDVRLLLNNDNLLRE.GAA.A.AQYN.D..TPVKIE
Retrocopy MADFEHCVSDDEKVA<IAAKSAPPPPRGEFNEVFNDVRLLLNNDNLLRE>GAAHAFAQYNMDQLTPVKIE

Parental  AYEDQVLITEHGDLGNGKFLDPKNRICFKFDHLRKEATDPRPYEAENAVESWRTSVETALRAYVKEHYPN
          .YE.QVLITEHGDLGN..FLDPKN.I.FKFDHL.KEA.DP.P.EA.....SWR.S...ALRAYVK.HY..
Retrocopy GYEEQVLITEHGDLGNSRFLDPKNKISFKFDHLPKEASDPHPEEADGGLKSWRESYDSALRAYVKDHYSH

Parental  GVCTVYGKKIDGQQTIIACIESHQFQAKNFWNGRWRSEWKFTISPSSTQVVGILKIQVHYYEDGNVQLVS
          G.CTVY.K.IDGQQTIIACIESHQFQ..NFWNGRWRS.WKFTI.P...QVVG.LKIQVHYYEDGNVQL.S
Retrocopy GFCTVYAKTIDGQQTIIACIESHQFQPQNFWNGRWRSQWKFTITPPTAQVVGVLKIQVHYYEDGNVQLSS

Parental  HKDIQDSLTVSNEAQTAKEFIKIVEAAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYK
          HKD..DS.TVSN...TAKEFIKI.E.AENEYQTAISENYQTMSDTTFKAL..QLPVT.TKIDWNKILSYK
Retrocopy HKDVRDSVTVSN*VPTAKEFIKIIEHAENEYQTAISENYQTMSDTTFKALHWQLPVTHTKIDWNKILSYK

Parental  IGKEMQNA
          IGKEMQNA
Retrocopy IGKEMQNA

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	0.00 RPM	101.68 RPM
SRP017611_kidney	0.00 RPM	92.27 RPM
SRP017611_liver	0.16 RPM	43.73 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_482 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 14 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004925	2 retrocopies	retro_chof_2296, retro_chof_680,
Cavia porcellus	ENSCPOG00000007677	1 retrocopy	retro_cpor_205,
Dasypus novemcinctus	ENSDNOG00000005771	1 retrocopy	retro_dnov_1892,
Dipodomys ordii	ENSDORG00000016226	1 retrocopy	retro_dord_266,
Erinaceus europaeus	ENSEEUG00000009063	5 retrocopies	retro_eeur_142, retro_eeur_167, retro_eeur_351, retro_eeur_365, retro_eeur_482 ,
Echinops telfairi	ENSETEG00000019711	3 retrocopies	retro_etel_1516, retro_etel_2020, retro_etel_442,
Gorilla gorilla	ENSGGOG00000012158	1 retrocopy	retro_ggor_1774,
Microcebus murinus	ENSMICG00000000707	1 retrocopy	retro_mmur_1224,
Myotis lucifugus	ENSMLUG00000007910	1 retrocopy	retro_mluc_2595,
Oryctolagus cuniculus	ENSOCUG00000003591	2 retrocopies	retro_ocun_1531, retro_ocun_873,
Pongo abelii	ENSPPYG00000017933	1 retrocopy	retro_pabe_1321,
Sus scrofa	ENSSSCG00000026942	2 retrocopies	retro_sscr_1127, retro_sscr_600,
Ictidomys tridecemlineatus	ENSSTOG00000024828	1 retrocopy	retro_itri_1561,
Tupaia belangeri	ENSTBEG00000012657	2 retrocopies	retro_tbel_2004, retro_tbel_2228,