RetrogeneDB ID: retro_ggor_2596

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:57775924..57776412(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSGGOG00000016840
• Aliases: None
• Description: None

Sequence

>retro_ggor_2596
TTCCAAGGAATAGTGTTGTCAATGAAGAAAGTAGCAGGGATGGATGTGGAGCTGACAGTTGAAGAAAGAAACCTCCTATC
TGTTTCATATAACAATGTGATTGAAGCTAGAAGAGCCTTCTGGAGAATAATCAGCATTGAACAGAAAGAACAAAACAAGG
GAGAAGACAAGCTAAAAATGATTTGGGAATATCAGCAAATGGTTGAGACTGAGCTGAAGTTAATCTGTTGTCACTTTCTG
TATGTACTGGACAAAACCTCATTCCAGCAGCTAACACTGGCGAGTCCAAGGTTTTCTATTATAAAATGAAAGGGGACTAC
CACAGGTATCTGGCAGAATTTGCCACAGGAAATGACAGGAAGGAGGCTGTGGAGAACAGCCTAGTGGGTTATAAAGCTGC
TAGTGATATTGCTATGACAGAACTTCCACCTGCGCATCCAATTCGCTTAAGTCTTGCTCTCAATTTTTCCTTATTCTACT
ACGAAATT

Alignment

ORF - retro_ggor_2596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.54 %
• Parental protein coverage: 64.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMV
          ....V.SMKKVAGMDVELTVEERNLLSV.Y.NVI.ARRA.WRIIS.IEQKE.NKG.EDKLKMI.EY.QMV
Retrocopy FQGIVLSMKKVAGMDVELTVEERNLLSVSYNNVIEARRAFWRIIS-IEQKEQNKG-EDKLKMIWEYQQMV

Parental  ETELKLICCDILDVLDK-HLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDI
          ETELKLICC..L.VLDK..LIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEA.ENSLV.YKAASDI
Retrocopy ETELKLICCHFLYVLDK<NLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAVENSLVGYKAASDI

Parental  AMTELPPTHPIRLGLALNFSVFYYEI
          AMTELPP.HPIRL.LALNFS.FYYEI
Retrocopy AMTELPPAHPIRLSLALNFSLFYYEI

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
SRP007412_brain_prefrontal_cortex	0.05 RPM	485.82 RPM
SRP007412_cerebellum	0.08 RPM	311.56 RPM
SRP007412_heart	0.03 RPM	81.05 RPM
SRP007412_kidney	0.08 RPM	261.16 RPM
SRP007412_liver	0.03 RPM	88.29 RPM
SRP007412_testis	1.45 RPM	444.96 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2596 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3851
Pan troglodytes	retro_ptro_2626
Pan troglodytes	retro_ptro_2624
Pan troglodytes	retro_ptro_2993

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005664	3 retrocopies	retro_btau_1485, retro_btau_372, retro_btau_954,
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Cavia porcellus	ENSCPOG00000008007	1 retrocopy	retro_cpor_307,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Dasypus novemcinctus	ENSDNOG00000003808	2 retrocopies	retro_dnov_1452, retro_dnov_2602,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Felis catus	ENSFCAG00000011368	1 retrocopy	retro_fcat_1636,
Homo sapiens	ENSG00000108953	4 retrocopies	retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Gorilla gorilla	ENSGGOG00000001569	1 retrocopy	retro_ggor_2081,
Gorilla gorilla	ENSGGOG00000004580	2 retrocopies	retro_ggor_2795, retro_ggor_699,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596 ,
Gorilla gorilla	ENSGGOG00000022133	9 retrocopies	retro_ggor_1092, retro_ggor_1754, retro_ggor_211, retro_ggor_2379, retro_ggor_2997, retro_ggor_2998, retro_ggor_3020, retro_ggor_499, retro_ggor_544,
Monodelphis domestica	ENSMODG00000010174	2 retrocopies	retro_mdom_1567, retro_mdom_744,
Nomascus leucogenys	ENSNLEG00000000656	2 retrocopies	retro_nleu_2067, retro_nleu_2868,
Otolemur garnettii	ENSOGAG00000006155	2 retrocopies	retro_ogar_1003, retro_ogar_2144,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,
Pan troglodytes	ENSPTRG00000008521	5 retrocopies	retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Ictidomys tridecemlineatus	ENSSTOG00000005084	1 retrocopy	retro_itri_1175,
Vicugna pacos	ENSVPAG00000010288	3 retrocopies	retro_vpac_230, retro_vpac_411, retro_vpac_559,