RetrogeneDB ID: retro_pabe_2491

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:170569200..170570438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA5
• Ensembl ID: ENSPPYG00000019609
• Aliases: HSPA5, GRP78
• Description: 78 kDa glucose-regulated protein precursor [Source:RefSeq peptide;Acc:NP_001126927]

Sequence

>retro_pabe_2491
CGCATCACGCGGTGCTATGTGGCCTTCACTCTTGAAGGGGAACATGTGATCGGCGATGCTGCCAAGAACCAGCTCACCTC
CAATCCCAAGAACACGGTCTTTGACGCCAACTGGTTCATCGGCCGCACGTGGAAAGACCTGTCTGTGTAGCAGAACATCA
GGTTCTTGCCGTTCAAGTTAGTCGAAAAGAAAACTAAACCAAACATTCAAGCTGATATTGGAGGTGGGCAAAGACACCTG
CTCCTGAAGAAATTTCTGCCATGGTTCTCACTGAAATGAAATGAACCGCTGAGGCTTATTTGAGAAAGAAGTTTACCCAT
GCAGTTGTTACCTTTCCAGCCTATTTCAATGATGCCCAGTGCCAAGCAACCAAAGACATTGGAACTATTGCTGAGCTAAA
TGTTATGAGGATCATCCACGAGCCTATGGCAGCTGCTATTGCTTATGGCCTGGATAAGAGAGAGAGGGAGAAGACATCCC
GTTGTTCCACCTGGGTGGCAGAACCTTCAATGCGTCTCCTCTCACCATTGACAATGGTGTCTTCGGAGTCGTGGCCACTA
ATGGAGATACTCATCTGGGTGGAGAAGCCTTTGACCAGCGTGTCATGGAACATTTCATCAAGTTGTACCAAAAGAAGACT
GACAAAGATGTCAGGAAAGATGATAGGGCTGTGCAGAAACTCCAGCTACAGGTAGAAAAGGCCAAACGGGCCCTGTCTCC
TCAACATCAAGCAAGAATTGAAATTGAGTCCTTCTGTGAAGGAGAAGACTTTTCTGAGACCCTGGCTCGGGCCAAATTTT
AAGAGCTAAAACATGGATCTGTTCCGGTCTACTATGAAGCCTGTCCAGAAAGTGTTGGAAAATTCTGATTTGAAGAATTC
TGATATTGATGAAGTTGTTCTTGGTGGCTCTACTCAAATTCCAAAGATTCCACAACTGGTTAAAAAGTCCTTCAATGGCA
AGGAGTCCTCCCATGGCATAAACCCAGATGAAGCTGTAGTGCGTGGTGCTGCTGTCCAGGCTGGAGTGCTCTCTGGTGAT
CAAGATACAGGTGACCTGGTACTGCTTGATGTATGTCCCCTTACACTTGGTATTGAAACTGTGGGAGGTGTCATGATCAA
ACTGATTCCAAGGAACACAGTGGTGCCTACCAAGAACTCTCAGATCTTTTCTACAGCTTCTGATAATCAACTAACTGTCA
CAATCAAGGTCTACGAGGATGAACGACCCCTGACAAGA

Alignment

ORF - retro_pabe_2491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.62 %
• Parental protein coverage: 63.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQ
          RIT..YVAFT.EGE..IGDAAKNQLTSNP.NTVFDA...IGRTW.D.SV.Q.I.FLPFK.VEKKTKP.IQ
Retrocopy RITRCYVAFTLEGEHVIGDAAKNQLTSNPKNTVFDANWFIGRTWKDLSV*QNIRFLPFKLVEKKTKPNIQ

Parental  VDIGGGQ-TKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRI
          .DI.GG...KT.APEEISAMVLT.MK.TAEAYL.KK.THAVVT.PAYFNDAQ.QATKD.GTIA.LNVMRI
Retrocopy ADI-GGG<AKTPAPEEISAMVLTEMK*TAEAYLRKKFTHAVVTFPAYFNDAQCQATKDIGTIAELNVMRI

Parental  INEPTAAAIAYGLDKREGEK-NILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFI
          I.EP.AAAIAYGLDKRE.EK..I..F.LGG.TF..S.LTIDNGVF.VVATNGDTHLGGE.FDQRVMEHFI
Retrocopy IHEPMAAAIAYGLDKREREK<DIPLFHLGGRTFNASPLTIDNGVFGVVATNGDTHLGGEAFDQRVMEHFI

Parental  KLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDFSETLTRAKFEEL-NMDLFR
          KLY.KKT.KDVRKD.RAVQKL...VEKAKRALS.QHQARIEIESF.EGEDFSETL.RAKF.EL.NMDLFR
Retrocopy KLYQKKTDKDVRKDDRAVQKLQLQVEKAKRALSPQHQARIEIESFCEGEDFSETLARAKF*EL>NMDLFR

Parental  STMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLS
          STMKPVQKVLE............VL.GGST.IPKI.QLVK..FNGKE.S.GINPDEAV..GAAVQAGVLS
Retrocopy STMKPVQKVLEXXXXXXXXXXXVVL-GGSTQIPKIPQLVKKSFNGKESSHGINPDEAVVRGAAVQAGVLS

Parental  GDQDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVVPTKKSQIFSTASDNQPTVTIKVYEGERPLTK
          GDQDTGDLVLLDVCPLTLGIETVGGVM.KLIPRNTVVPTK.SQIFSTASDNQ.TVTIKVYE.ERPLT.
Retrocopy GDQDTGDLVLLDVCPLTLGIETVGGVMIKLIPRNTVVPTKNSQIFSTASDNQLTVTIKVYEDERPLTR

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	193.90 RPM
SRP007412_cerebellum	0.24 RPM	166.47 RPM
SRP007412_heart	0.06 RPM	309.67 RPM
SRP007412_kidney	0.07 RPM	512.98 RPM
SRP007412_liver	0.34 RPM	1997.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2491 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2491 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3005
Pan troglodytes	retro_ptro_2033
Gorilla gorilla	retro_ggor_2082
Callithrix jacchus	retro_cjac_2221

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006880	1 retrocopy	retro_cjac_2221,
Homo sapiens	ENSG00000044574	1 retrocopy	retro_hsap_3005,
Gallus gallus	ENSGALG00000001000	1 retrocopy	retro_ggal_21,
Gorilla gorilla	ENSGGOG00000026879	1 retrocopy	retro_ggor_2082,
Macropus eugenii	ENSMEUG00000016702	1 retrocopy	retro_meug_522,
Mus musculus	ENSMUSG00000026864	1 retrocopy	retro_mmus_1299,
Nomascus leucogenys	ENSNLEG00000017348	1 retrocopy	retro_nleu_751,
Otolemur garnettii	ENSOGAG00000006786	1 retrocopy	retro_ogar_2901,
Pongo abelii	ENSPPYG00000003987	9 retrocopies	retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pongo abelii	ENSPPYG00000019609	1 retrocopy	retro_pabe_2491 ,
Pan troglodytes	ENSPTRG00000000563	1 retrocopy	retro_ptro_2033,
Ictidomys tridecemlineatus	ENSSTOG00000011243	4 retrocopies	retro_itri_1686, retro_itri_1687, retro_itri_1689, retro_itri_1879,