RetrogeneDB ID: retro_pabe_1950

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:48307089..48307759(+)
• 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_1950
TACAAGGTCATTTTTGTGCAAGAAGGTGGGTCTGGCCAGTTCAGTGCTGTCCCCTAGTGCCTGAAAGCAGGAAGGTGTGC
CAACTATGTGGTGAGAGAAGCTTGGTCAGCTAAAGCTGCAGAAGCATCCAAGAAGTTTGAGATTGTGAATATCAGCTACC
CTAAACTTGGGAGTTATATGAAAATTCCAGATTCAACACCTGGAACCTCACCCTTACAGCTTCTATGTGTAATGCTGCAC
AAATGACTGGCACAGAGTGGCGTTTGACTTTATATCTGATCTCAGGAAGCACTACTGGTTTGCCACATATCCTCAAACTT
CCTATCGAAGGCAGTGGATGCTTCCAGGTTTGGTGTGATTTTTGCTGGTGCCCAGAAGCATGTTGGTTGTTTTGGGATGA
CAGTAGTGATCATCTGCAATGACTGCTGGGGTCACCCTCAGAGAATGGCCCTCCATCCTGGAATACAAAGTGCATGTTGG
AAACAACTTCTTGTACAAGATGCGACAGTATTTCAGCAACTATGTCATGGGCTTGTTCCTGGTGTAGATTAAGAATGATG
GCACTGCAGCAGTGATGGAGAAGCTTAGCTTCATCAACTCTAAAATAATAATTTATGATATTTTTAATAATTCTTAAGGA
TTCTGTGAATGTCCAGTAAAGCCTCATAAT

Alignment

ORF - retro_pabe_1950 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.97 %
• Parental protein coverage: 54.94 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YKVIFLQGGGSGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDP-S
          YKVIF.Q.GGSGQFSAVP..L...KAGRCA.YVV..AWSAKAAE..KKF...NI..PKLGSY.KIPD...
Retrocopy YKVIFVQEGGSGQFSAVP*CL---KAGRCANYVVREAWSAKAAEASKKFEIVNISYPKLGSYMKIPDS<N

Parental  TWNL-NPDASYVYYCANETVHGVEFDFIPDVK-GAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAG
          TWNL..P...YV..C.N...H.V.FDFI.D....A.LVC..SSNFLSK.VD.S.FGVIFAGAQK.VG..G
Retrocopy TWNL<HPYSFYV*CCTNDW-HRVAFDFISDLR<EALLVCHISSNFLSKAVDASRFGVIFAGAQKHVGCFG

Parental  VTVVIVRDD-LLG-FALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGATAMEKLSSTK
          .TVVI...D.LLG...LRE.PS.LEYKV..GN..LY.....FS.YVMGL.L..IKN.G.A..MEKLS...
Retrocopy MTVVIICND<LLG<VTLREWPSILEYKVHVGNNFLYKMRQYFSNYVMGLFLV*IKNDGTAAVMEKLSFIN

Parental  SQ-TIYEIIDNSQGFYVCPVEPQN
          S...IY.I..NS.GF..CPV.P.N
Retrocopy SKIIIYDIFNNS*GFCECPVKPHN

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	0.00 RPM	12.88 RPM
SRP007412_cerebellum	0.12 RPM	10.21 RPM
SRP007412_heart	0.00 RPM	0.33 RPM
SRP007412_kidney	0.03 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_1950 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1950 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1950 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2267
Pan troglodytes	retro_ptro_1606
Callithrix jacchus	retro_cjac_1203

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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,