RetrogeneDB ID: retro_eeur_416

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_292433:302..910(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHA3
• Ensembl ID: ENSEEUG00000004169
• Aliases: None
• Description: pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3 [Source:HGNC Symbol;Acc:14338]

Sequence

>retro_eeur_416
CTGATAGATACTAGGACTAAAAAGGAAAAAGAAATAAATGAAACTAGTGAATCTTTGAAAACCAAAATGTCTGAACTTCG
TCTCTACTGTGACCTCTTAATGCAGCAAGTTCATACAATCCAAGTGTTTGTTCACCATAACAAGAATAATTCACCTCCCA
GAATAGAGAACATGAATGAAGCTTCTTTTCTGCTGAGTGCCACATGTGATACATTCATCACAACCTTCGAAGAATGTGTG
AAGATAGCAAATGTGAAGTTTAAGCCTGAAATGTTTTCAGCTCACCCATCAGGATCTCCTACTTTCTCATGTGTCACCTT
CTCCTGTCCAAATGATGAAGCGTTCTGTCAGTCACCCTGGTTCTTGCAGTTCAGAGAGGACTAGTCACCCTATGAAAGAA
CCAGTGCCTACATTTTATCGGTTCTCACAGAGACACCGAAGAACAGACATGCACACCTGTAATGATATTCCTCTTGAAGA
TCCAAATCAACCTGTTTACTGTTCAAGAAGTCCACTTAATGGAGATTTGGCTTCAGAAACCATTCCTGAAGAAAAGCAGA
CTTATGGCCAAGAGAAAGTCTGAATCTAAAGATCTTCTACCATCCTTC

Alignment

ORF - retro_eeur_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.5 %
• Parental protein coverage: 82.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTDTRTKG-KEINETSESLKTKMSELRLYCDLLMQQVHTIQEFVHHDENHSPPSIENMNEASSLLSATCN
          L.DTRTK..KEINETSESLKTKMSELRLYCDLLMQQVHTIQ.FVHH..N.SPP.IENMNEAS.LLSATC.
Retrocopy LIDTRTKKEKEINETSESLKTKMSELRLYCDLLMQQVHTIQVFVHHNKNNSPPRIENMNEASFLLSATCD

Parental  TFITTLEECVKIANAKFKPEM-FQLTHPDPLVSPVSPSPVQMMKRSVSHPGSCSSERTSHPMKEPVPTFY
          TFITT.EECVKIAN.KFKPEM.FQLTH.D.L.S.VSPSPVQMMKRSVSHPGSCSSERTSHPMKEPVPTFY
Retrocopy TFITTFEECVKIANVKFKPEM>FQLTHQDLLLSHVSPSPVQMMKRSVSHPGSCSSERTSHPMKEPVPTFY

Parental  RFSQRRRRTYSDTDTCNDIPLEDPDRPVHCSRSTLNGDLAPVTIPEE-SKLTAKKTSESEDLLPSF
          RFSQR.RRT..D..TCNDIPLEDP..PV.CSRS.LNGDLA..TIPEE.S.L.AK..SES.DLLPSF
Retrocopy RFSQRHRRT--DMHTCNDIPLEDPNQPVYCSRSPLNGDLASETIPEE>SRLMAKRKSESKDLLPSF

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	46.57 RPM
SRP017611_kidney	1.13 RPM	27.01 RPM
SRP017611_liver	0.00 RPM	5.31 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_416 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 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013997	5 retrocopies	retro_chof_1366, retro_chof_1559, retro_chof_300, retro_chof_736, retro_chof_985,
Cavia porcellus	ENSCPOG00000003906	1 retrocopy	retro_cpor_487,
Dasypus novemcinctus	ENSDNOG00000002717	1 retrocopy	retro_dnov_107,
Erinaceus europaeus	ENSEEUG00000004169	1 retrocopy	retro_eeur_416 ,
Homo sapiens	ENSG00000116095	1 retrocopy	retro_hsap_2060,
Macropus eugenii	ENSMEUG00000015317	2 retrocopies	retro_meug_1530, retro_meug_341,
Microcebus murinus	ENSMICG00000009898	1 retrocopy	retro_mmur_617,
Myotis lucifugus	ENSMLUG00000005823	2 retrocopies	retro_mluc_1031, retro_mluc_689,
Oryctolagus cuniculus	ENSOCUG00000005495	1 retrocopy	retro_ocun_1273,
Otolemur garnettii	ENSOGAG00000002724	1 retrocopy	retro_ogar_1845,
Tupaia belangeri	ENSTBEG00000007550	3 retrocopies	retro_tbel_4186, retro_tbel_4555, retro_tbel_4723,
Tarsius syrichta	ENSTSYG00000005341	1 retrocopy	retro_tsyr_869,
Tursiops truncatus	ENSTTRG00000009729	2 retrocopies	retro_ttru_1296, retro_ttru_1497,
Vicugna pacos	ENSVPAG00000003490	3 retrocopies	retro_vpac_487, retro_vpac_578, retro_vpac_619,