RetrogeneDB ID: retro_pabe_657

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10_random:31784376..31785303(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERGIC2
• Ensembl ID: ENSPPYG00000004390
• Aliases: None
• Description: ERGIC and golgi 2 [Source:HGNC Symbol;Acc:30208]

Sequence

>retro_pabe_657
TTAAGTTTGGTAAAAGAGTTGGATGTCTTTCCAAAGGTTCCTGAGAGCTATGTAGAGACTTCAGCCTGCGGAGGTACGGT
TTCTCTAATAGCATTTACAACTATGGCTTTATTAACCATAATGGAATTCTCAGTATATCAAGATACATGGATGAAGTATG
AATATGAAGTAGACAAGGATTTTTCTAGCAAATTGAGAATCAATATAGATATTACTGTTGCCATGAAGTGTCAATATCTT
GGAGCGGATGTATTGGATTTAGCAGAAACAATGGTTGCATCTGCAGATAGTCTAGTTTATGAACCAACAGTATTTGGTCT
TTCACCACAGCAGAAAGAGTGGCAGAGGATGCTGCAGCTGATTCAGAGTAGGCTACAAGAAGAGCATTCAATTCAAGTTG
TGATATTTAAAAGTGCTTTTAAAAGTGCATCGACAGCTCTTCCACCAAGAGAAGATGATTCATCACATACTCCAGATGCA
TGCAGAATTCATGGCCATTTATATGTCAATAAAGTAGCAGGGAATTTTCACATAACAGTGGGCAAGGCAATTCCACATCC
TCGTGGTCATACACATTTGGCAGCACTTGTCAACCATGAATCTTACAATTTTTCTCATAGAAAAGATCATTTGTCTTTTG
GAGAGCTTGTTCCAGCAACTATTAATCCTTTAGATGGAACTGAAAAAATTGCTATAGATCACAACCAGATGTTACAATAT
TTTATTACATTTGTGTCAACAAAACTATGTACATAAAAAATATCAGCAGTCACCCATCAGTTTTCTGTGACAGGAAGGGA
ATGTATCATTAACCATGCTGCAGGCAACCATGGAGTCTCTGGGATATTTATGAAATATGATCTCAGTTCTCTTATGGTGA
CAGTTACTGAGGAGCGCATGCCATTCTGGCAGTTTTTTGTAAGACTC

Alignment

ORF - retro_pabe_657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.23 %
• Parental protein coverage: 80.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSLVKELDAFPKVPESYVETSASGGTVSLIAFTTMALLTIMEFSVYQDTWMKYEYEVDKDFSSKLRINID
          LSLVKELD.FPKVPESYVETSA.GGTVSLIAFTTMALLTIMEFSVYQDTWMKYEYEVDKDFSSKLRINID
Retrocopy LSLVKELDVFPKVPESYVETSACGGTVSLIAFTTMALLTIMEFSVYQDTWMKYEYEVDKDFSSKLRINID

Parental  ITVAMKCQF-GADVLDLAETMVASADGLVYEPTVFDLSPQQKEWQRMLQLIQSRLQEEHSLQDVIFKSAF
          ITVAMKCQ..GADVLDLAETMVASAD.LVYEPTVF.LSPQQKEWQRMLQLIQSRLQEEHS.Q.VIFKSAF
Retrocopy ITVAMKCQYLGADVLDLAETMVASADSLVYEPTVFGLSPQQKEWQRMLQLIQSRLQEEHSIQVVIFKSAF

Parental  KSASTALPPREDDSSQSPDACRIHGHLYVNKVAGNFHITVGKAIPHPRGHAHLAALVNHESYNFSHRIDH
          KSASTALPPREDDSS..PDACRIHGHLYVNKVAGNFHITVGKAIPHPRGH.HLAALVNHESYNFSHR.DH
Retrocopy KSASTALPPREDDSSHTPDACRIHGHLYVNKVAGNFHITVGKAIPHPRGHTHLAALVNHESYNFSHRKDH

Parental  LSFGELVPAIINPLDGTEKIAIDH-QMFQYFITVVPTKLHTYKISADTHQFSVTERERIINHAAGSHGVS
          LSFGELVPA.INPLDGTEKIAIDH.QM.QYFIT.V.TKL.T.KISA.THQFSVT.RE.IINHAAG.HGVS
Retrocopy LSFGELVPATINPLDGTEKIAIDHNQMLQYFITFVSTKLCT*KISAVTHQFSVTGRECIINHAAGNHGVS

Parental  GIFMKYDLSSLMVTVTEEHMPFWQFFVRL
          GIFMKYDLSSLMVTVTEE.MPFWQFFVRL
Retrocopy GIFMKYDLSSLMVTVTEERMPFWQFFVRL

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	0.44 RPM	8.85 RPM
SRP007412_cerebellum	0.36 RPM	10.82 RPM
SRP007412_heart	0.42 RPM	8.37 RPM
SRP007412_kidney	0.33 RPM	6.43 RPM
SRP007412_liver	0.55 RPM	11.20 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_657 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_657 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015668	1 retrocopy	retro_cpor_824,
Ornithorhynchus anatinus	ENSOANG00000010582	1 retrocopy	retro_oana_32,
Oryctolagus cuniculus	ENSOCUG00000017255	1 retrocopy	retro_ocun_1540,
Pongo abelii	ENSPPYG00000004390	1 retrocopy	retro_pabe_657 ,
Rattus norvegicus	ENSRNOG00000001852	1 retrocopy	retro_rnor_1557,
Sarcophilus harrisii	ENSSHAG00000004822	1 retrocopy	retro_shar_386,
Tupaia belangeri	ENSTBEG00000011223	1 retrocopy	retro_tbel_3783,