RetrogeneDB ID: retro_pabe_2940

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:30002350..30002943(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1A
• Ensembl ID: ENSPPYG00000002374
• Aliases: None
• Description: GTP-binding protein SAR1a [Source:UniProtKB/Swiss-Prot;Acc:Q5R548]

Sequence

>retro_pabe_2940
ATGTCTTTCCTCTTTGAGTGGATCTACGATGGCTTCAGCAGTGTGCTCCAGTTCCTAGGACTCTACAAGAAATTTGGAAA
ACTTGTATTTTTGGGTTTGGACAATGCAGGCAAAACCACTCTTCTTCACATGCTCAAAGATGACAGATTGGGTCAACATG
TTCCAACACTACATCCGACATCAGAAAAGCTAATAATTGCTGGAATGACTTTTACAACTTTTGATCTTGGTGGACACAAG
CAAGCATGTCAGGTTTGAAAAAATTGTCTCCCAGCAATTAATGAGATTGTTTTTCTGGTGGATTCTGCAGATCATTCTGG
CCTCATGGAATCTAAAGTTGAGCTTAATGCTTTAATCACTGATGAAATAATATCCAATGTGCCAATCCTTATCTTGGGTA
ACAAAATAGACAGAACAATGCAATCAGTGAAGAAAAACTCTTTGAGATATTTGGGCTTTCTGGACAGACCACAGGAAAGA
GGAACATGGCCCTTTAGGAGCTGAACGCTCACCCCATGGAAGTGTTCATGTGCAGTGTGCTCAAGAGGCAAGGCTAGGGT
GAGGGATTCTGCTGGCTCTCCCAATATATTGAC

Alignment

ORF - retro_pabe_2940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.43 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSFIFEWIYNGFSSVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMT
          MSF.FEWIY.GFSSVLQFLGLYKK.GKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSE.L.IAGMT
Retrocopy MSFLFEWIYDGFSSVLQFLGLYKKFGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEKLIIAGMT

Parental  FTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHSRLVESKVELNALMTDETISNVPILILGNKIDRT-
          FTTFDLGGH.QA..V.KN.LPAIN.IVFLVD.ADHS.L.ESKVELNAL.TDE.ISNVPILILGNKIDRT.
Retrocopy FTTFDLGGHKQACQV*KNCLPAINEIVFLVDSADHSGLMESKVELNALITDEIISNVPILILGNKIDRT<

Parental  DAISEEKLREIFGLYGQTTGKGNVTLKELNARPMEVFMCSVLKRQGYGEGFRWLSQYID
          .AISEEKL.EIFGL.GQTTGK.N..L.ELNA.PMEVFMCSVLKRQG.GEGF.WLSQYID
Retrocopy NAISEEKLFEIFGLSGQTTGKRNMAL*ELNAHPMEVFMCSVLKRQG*GEGFCWLSQYID

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	70.16 RPM
SRP007412_cerebellum	0.00 RPM	63.96 RPM
SRP007412_heart	0.00 RPM	38.23 RPM
SRP007412_kidney	0.00 RPM	65.27 RPM
SRP007412_liver	0.00 RPM	74.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2940 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2940 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3568
Pan troglodytes	retro_ptro_2423
Macaca mulatta	retro_mmul_1825

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016353	5 retrocopies	retro_cjac_1006, retro_cjac_2242, retro_cjac_2305, retro_cjac_4081, retro_cjac_957,
Homo sapiens	ENSG00000079332	4 retrocopies	retro_hsap_2976, retro_hsap_3568, retro_hsap_4714, retro_hsap_639,
Gorilla gorilla	ENSGGOG00000024879	3 retrocopies	retro_ggor_144, retro_ggor_2408, retro_ggor_2929,
Myotis lucifugus	ENSMLUG00000006626	2 retrocopies	retro_mluc_1317, retro_mluc_1996,
Nomascus leucogenys	ENSNLEG00000011243	4 retrocopies	retro_nleu_1987, retro_nleu_2231, retro_nleu_2311, retro_nleu_2759,
Otolemur garnettii	ENSOGAG00000005040	3 retrocopies	retro_ogar_1447, retro_ogar_1981, retro_ogar_2467,
Pongo abelii	ENSPPYG00000002374	4 retrocopies	retro_pabe_2468, retro_pabe_2940 , retro_pabe_3661, retro_pabe_565,
Pan troglodytes	ENSPTRG00000002584	4 retrocopies	retro_ptro_2011, retro_ptro_2423, retro_ptro_3133, retro_ptro_465,
Ictidomys tridecemlineatus	ENSSTOG00000012780	2 retrocopies	retro_itri_1191, retro_itri_590,
Tupaia belangeri	ENSTBEG00000008657	5 retrocopies	retro_tbel_1060, retro_tbel_14, retro_tbel_2319, retro_tbel_2366, retro_tbel_2846,
Tarsius syrichta	ENSTSYG00000005955	2 retrocopies	retro_tsyr_1204, retro_tsyr_2099,
Vicugna pacos	ENSVPAG00000002631	2 retrocopies	retro_vpac_5, retro_vpac_77,