RetrogeneDB ID: retro_pabe_308

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:150029546..150030176(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSAT1
• Ensembl ID: ENSPPYG00000019313
• Aliases: None
• Description: phosphoserine aminotransferase 1 [Source:HGNC Symbol;Acc:19129]

Sequence

>retro_pabe_308
CCAGGAAGGCTAGCCTTTCACGTGTTCGGTCCTCCTTGGCTGACTCGCCGCCCTTGCTGCCGCACCGTGGACGCCCCGAG
GCACGTGGTCAACCTCGGGCCTGGTCCCGCCAAGCTGCCTCACTCAGTGTTGTTAGAGATAAAAAAGGAATTATTAGACT
ACAGAGGAGTTGGCATTAGTGTTCTTGAAATGAGTCACAGGCCATCAGATTTTGCCAAGATTATTAACAATACAGAGAAT
CTTGTGCGGGAATTGCTAGCCGTTCCAGACAGCTATAAGGTGATTTTTGTGCAAGGAAGTGGGTCCGGCCAGTTCGGTGC
CGTCCCCTTAAACCTGATTGGCTTGAAAGCAGGAACATGTGCGGACTATGTGGTGACAGGAGCTTGGTCAGCTAAGGCCG
CAGAAGCAGCCAAGAAGTTTGGGACTATAAATATCATTCACCCTAAACTTGGGAGTTATACAAAAATTCAAGATCCAAGC
ACCTGGAACCTCAACCCGGATGCCTCTTACGTGTATTATTGCGCAAATGAGATGGTGCATGGTGTGGAGTTTGACTTTAT
ACCCGATGTCAAGGGAGCAGTACTGGTTTGTGACATGTCCTCAAACTTCCTGTCCAAGCCAGTGGATGTC

Alignment

ORF - retro_pabe_308 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.52 %
• Parental protein coverage: 50.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGTPAVHAFGPPWLTHRPRRRTMDAPRQVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMSHRSSD
          PG..A.H.FGPPWLT.RP..RT.DAPR.VVN.GPGPAKLPHSVLLEI.KELLDY.GVGISVLEMSHR.SD
Retrocopy PGRLAFHVFGPPWLTRRPCCRTVDAPRHVVNLGPGPAKLPHSVLLEIKKELLDYRGVGISVLEMSHRPSD

Parental  FAKIINNTENLVRELLAVPDNYKVIFLQGGGSGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKF
          FAKIINNTENLVRELLAVPD.YKVIF.QG.GSGQF.AVPLNLIGLKAG.CADYVVTGAWSAKAAE.AKKF
Retrocopy FAKIINNTENLVRELLAVPDSYKVIFVQGSGSGQFGAVPLNLIGLKAGTCADYVVTGAWSAKAAEAAKKF

Parental  GTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDV
          GTINI.HPKLGSYTKI.DPSTWNLNPDASYVYYCANE.VHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDV
Retrocopy GTINIIHPKLGSYTKIQDPSTWNLNPDASYVYYCANEMVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDV

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	0.06 RPM	12.88 RPM
SRP007412_cerebellum	0.00 RPM	10.21 RPM
SRP007412_heart	0.00 RPM	0.33 RPM
SRP007412_kidney	0.07 RPM	74.61 RPM
SRP007412_liver	0.00 RPM	29.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_308 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_308 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_412
Pan troglodytes	retro_ptro_316
Gorilla gorilla	retro_ggor_407

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006898	1 retrocopy	retro_amel_375,
Bos taurus	ENSBTAG00000013960	1 retrocopy	retro_btau_1658,
Canis familiaris	ENSCAFG00000001570	1 retrocopy	retro_cfam_269,
Choloepus hoffmanni	ENSCHOG00000003817	1 retrocopy	retro_chof_2702,
Callithrix jacchus	ENSCJAG00000003319	1 retrocopy	retro_cjac_1203,
Echinops telfairi	ENSETEG00000004158	1 retrocopy	retro_etel_99,
Homo sapiens	ENSG00000135069	3 retrocopies	retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Loxodonta africana	ENSLAFG00000017917	2 retrocopies	retro_lafr_1249, retro_lafr_660,
Macaca mulatta	ENSMMUG00000011868	2 retrocopies	retro_mmul_1029, retro_mmul_2341,
Mustela putorius furo	ENSMPUG00000012566	1 retrocopy	retro_mputfur_808,
Nomascus leucogenys	ENSNLEG00000002989	3 retrocopies	retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus	ENSOCUG00000007765	1 retrocopy	retro_ocun_1092,
Pongo abelii	ENSPPYG00000019313	3 retrocopies	retro_pabe_1950, retro_pabe_308 , retro_pabe_3328,
Pan troglodytes	ENSPTRG00000021045	2 retrocopies	retro_ptro_1606, retro_ptro_316,
Rattus norvegicus	ENSRNOG00000013971	1 retrocopy	retro_rnor_1663,
Tupaia belangeri	ENSTBEG00000012946	1 retrocopy	retro_tbel_1577,
Tarsius syrichta	ENSTSYG00000000093	2 retrocopies	retro_tsyr_1073, retro_tsyr_1212,