RetrogeneDB ID: retro_ptro_2538

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:62684687..62685281(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSPTRG00000008521
• Aliases: None
• Description: Pan troglodytes tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (YWHAE), mRNA. [Source:RefSeq mRNA;Acc:NM_001246368]

Sequence

>retro_ptro_2538
TTCCAAGAAATGGTGTAGTCAATGAAGAAAGTAGCAGGGATGGATGTGGAACTGACAGTTGAAGAAATAAACTTCCCATC
TGTTGCATATAAGAATGTAATTGGAGCTAGAAGAGCCTCCTGGAGAATAATCAGCAGTATTGAACAGAAAGAAGAAAACA
AGGAAGGAGAAGACAAGCTAAAAATGATTTGGGAATATCAGCAAATGATTGAGACTGAGCTAAAGTTACTCTGTTGTGAC
ATTCTGGATGTACTGGACAAAAACCTCATTCCAGCAGCTAACACTGGCGAGTCCAAAGTTTTCTATTATAAAATGAAAGG
GGACTACCACAGGTATCTGGCAGAATTTGCCACAGGAAATGACAGGAAGGAGGCTGTGGAGAACAGCCTAGTGGCTTATA
AACTGCTAGTGATATTGCAATGACAGAACTTCCACCAATGCATCCTATTCGCTTAGGTCTTGCTCTCAAATTTTTCTGTA
TTCTACTACGAAATTCTTAATTCCCCTGACCATGCCTGCAGGTTGGCAAAAGCAGCTTTTGATGATACAATTGCAGAACT
GGATACGCTGAGTGAAGAAAGCTATAAGGACACT

Alignment

ORF - retro_ptro_2538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 77.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMV
          ..EMV.SMKKVAGMDVELTVEE.N..SVAYKNVIGARRASWRIISSIEQKEENK.GEDKLKMI.EY.QM.
Retrocopy FQEMV*SMKKVAGMDVELTVEEINFPSVAYKNVIGARRASWRIISSIEQKEENKEGEDKLKMIWEYQQMI

Parental  ETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYK-AASDI
          ETELKL.CCDILDVLDK.LIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEA.ENSLVAYK..ASDI
Retrocopy ETELKLLCCDILDVLDKNLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAVENSLVAYK<TASDI

Parental  AMTELPPTHPIRLGLAL-NFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDS
          AMTELPP.HPIRLGLAL.NFSVFYYEILNSPD.ACRLAKAAFDD.IAELDTLSEESYKD.
Retrocopy AMTELPPMHPIRLGLAL>NFSVFYYEILNSPDHACRLAKAAFDDTIAELDTLSEESYKDT

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	0.11 RPM	546.12 RPM
SRP007412_cerebellum	0.22 RPM	571.39 RPM
SRP007412_heart	0.06 RPM	404.14 RPM
SRP007412_kidney	0.05 RPM	351.38 RPM
SRP007412_liver	0.07 RPM	235.52 RPM
SRP007412_testis	11.17 RPM	787.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2538 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2538 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3739

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 48 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,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Homo sapiens	ENSG00000108953	4 retrocopies	retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
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,
Pan troglodytes	ENSPTRG00000011641	2 retrocopies	retro_ptro_2032, retro_ptro_3,
Pan troglodytes	ENSPTRG00000013529	12 retrocopies	retro_ptro_1010, retro_ptro_1686, retro_ptro_2390, retro_ptro_2828, retro_ptro_2887, retro_ptro_3125, retro_ptro_3201, retro_ptro_3225, retro_ptro_412, retro_ptro_453, retro_ptro_594, retro_ptro_965,
Ictidomys tridecemlineatus	ENSSTOG00000005084	1 retrocopy	retro_itri_1175,
Vicugna pacos	ENSVPAG00000010288	3 retrocopies	retro_vpac_230, retro_vpac_411, retro_vpac_559,