RetrogeneDB ID: retro_ptro_465

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:125862911..125863507(+)
• Located in intron of: ENSPTRG00000003046

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1A
• Ensembl ID: ENSPTRG00000002584
• Aliases: None
• Description: SAR1 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10534]

Sequence

>retro_ptro_465
ATGTCTTTCATCTGTGAGTGGATCTACAATGGCTTCTACAGTGTGCTCCAGTTTCTAGGACTCTACAAGAAATCTAGTAA
ACTTGTTCTCTTGGGTTGGGACAATGTGGATGAAACCATTCTTCCTCATATGCTCAAAGATGGCGGATTGGGCCAACAGG
CTCCAACACGACCTCTGACATCAGCAGAGCTGACAACTGCTAGCCTGGCTTTTACAACTTTTGATCTTCTGGGGCATGAG
CAAACACGTTGGATTTGGAACAGTGATATCCCAGCAATAAATGGGATTGCCTTTCTGGGGTACTGTGCAGATTGTCCTCA
GATCCTGGAATCCAAAGTGGAGCTCAATGCTTCAATGACTGATGAAAGAATATCCCATGTGCCAGTCCTTATCTTGATTA
GCAAAAATTGGACAGAACAGGCACAATCAGTGAAGAAAAACTCTGTCTGCCATTTGGTCTTTATGGACAGACCACAGGAA
AGGGAACTCGTGACCCTGAAGGAGCCAAATGCCTTTTCCAAGGAATCGTTCACATTCAGTGTGTACAACAACAGGGCTAT
GGCAAGGGCTTCTGCTGGTTTGCCCAGTATATTGAC

Alignment

ORF - retro_ptro_465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSFIFEWIYNGFSSVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMT
          MSFI.EWIYNGF.SVLQFLGLYKKS.KLV.LG.DN...T.L.HMLKD..LGQ..PT...TS.ELT.A...
Retrocopy MSFICEWIYNGFYSVLQFLGLYKKSSKLVLLGWDNVDETILPHMLKDGGLGQQAPTRPLTSAELTTASLA

Parental  FTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHSRLVESKVELNALMTDETISNVP-ILILGN-KIDR
          FTTFDL.GHEQ.R..W....PAINGI.FL..CAD.....ESKVELNA.MTDE.IS.VP........K.DR
Retrocopy FTTFDLLGHEQTRWIWNSDIPAINGIAFLGYCADCPQILESKVELNASMTDERISHVPVLILISK<KLDR

Parental  TDAISEEKLREIFGLYGQTTGKGN-VTLKELNARPMEVFMCSV-LKRQGYGEGFRWLSQYID
          T..ISEEKL...FGLYGQTTGKG..VTLKE.NA...E.F..SV....QGYG.GF.W..QYID
Retrocopy TGTISEEKLCLPFGLYGQTTGKGT>VTLKEPNAFSKESFTFSV<VQQQGYGKGFCWFAQYID

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	52.44 RPM
SRP007412_cerebellum	0.00 RPM	60.94 RPM
SRP007412_heart	0.00 RPM	51.88 RPM
SRP007412_kidney	0.00 RPM	72.52 RPM
SRP007412_liver	0.00 RPM	64.45 RPM
SRP007412_testis	0.00 RPM	52.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_465 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_465 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_465 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_639
Pongo abelii	retro_pabe_565
Callithrix jacchus	retro_cjac_1006

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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,