RetrogeneDB ID: retro_pabe_2107

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:27264767..27265155(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSPPYG00000007769
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide [Source:HGNC Symbol;Acc:12851]

Sequence

>retro_pabe_2107
ATGGATGATCAAGAGGATCTGGTGTACCAGGCAAAGCTGGCCAAGCAGGCTGAGCGATATGACGAAATGGTGGAGTCAAT
GAAGAAAGTAGCAGGGATGGATGTGGAGCTGACAGTTGAAGAAAGAAACCTCCTATCACATTGCAAATAAGAATGTGATT
GAAGCTAGAAGAGCCTCCGGGAGAATAATCAGCAACGTTGAACAGAAAGAAGAAAACAAGGGAGGAGAAGACAAGCTAAA
AATGATTCGGGAATATCGGCAAATGGTTGAGACTGAGCTAAAGTTAATCTGTTGTGACATTCTGGATGTACTGGACAAAC
ACCTCATTCCAGCAGCTAACACTGGCGAGTCCAAGGTTTTCTATTATAAAATGAAAGGGGACTACCAT

Alignment

ORF - retro_pabe_2107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.08 %
• Parental protein coverage: 53.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLS-VAYKNVIGARRASWRIISSIEQK
          MDD.EDLVYQAKLA.QAERYDEMVESMKKVAGMDVELTVEERNLLS..A.KNVI.ARRAS.RIIS..EQK
Retrocopy MDDQEDLVYQAKLAKQAERYDEMVESMKKVAGMDVELTVEERNLLS>IANKNVIEARRASGRIISNVEQK

Parental  EENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYH
          EENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYH
Retrocopy EENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYH

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	1.49 RPM	551.30 RPM
SRP007412_cerebellum	0.24 RPM	371.37 RPM
SRP007412_heart	0.84 RPM	183.09 RPM
SRP007412_kidney	0.66 RPM	279.79 RPM
SRP007412_liver	0.43 RPM	168.13 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2107 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2107 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2324
Pan troglodytes	retro_ptro_1697

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 54 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	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,
Pongo abelii	ENSPPYG00000011041	5 retrocopies	retro_pabe_3453, retro_pabe_3454, retro_pabe_3519, retro_pabe_3520, retro_pabe_692,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391, retro_pabe_3511,
Pongo abelii	ENSPPYG00000018791	7 retrocopies	retro_pabe_103, retro_pabe_1242, retro_pabe_2047, retro_pabe_3417, retro_pabe_3740, retro_pabe_556, retro_pabe_89,
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,