RetrogeneDB ID: retro_pabe_1036

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:23350852..23352136(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPO7
• Ensembl ID: ENSPPYG00000029652
• Aliases: None
• Description: importin 7 [Source:HGNC Symbol;Acc:9852]

Sequence

>retro_pabe_1036
TTAAATCAGGGAGTTTCTCATGCTCTCACCTGGAAGAATCCAAAGCCCCATATACAAGGCATTATCCAAGATGTTATTTT
TCCATTGATGTGCTATACAGATGCTGATGAGGAACTTTGGCAAGAAGACCCTTACGAATATATCCGCATGAAGTTTGATG
TGTTTGAAGATTTCATTTCTCCTACCACTGCTGCCCAGACACTTTTGTTTACAGCCTGTAGTAAGAGGAAAGAGGTACTG
CAAAAGACTATGGGATTTTGTTACCAGATTCTTACAGAACCAAATGCTGACCCTCGAAAAAAAGATGGAGCCCTGCATAT
GATTGGCTCTTTAGCTGAAATACTTCTGAAGAAGAAGATCTATAAAGATCAGATGGAATGCATGTTGCAGAATCATGTAC
TCCCACTCTTTAGCAGTGAACTACGCTACATGAGAGCAAGGGCTTGTTGGGTACTTCACTATTTTTGTGAAGTGAAGTTC
GAAAGTGATCAGAACCTTCAAACAGCCTTAGAGCTAACAAGAAGATGTCTGATTGATGATAGAGAAATGCCTGTGAAAGT
GGAAGCTGCCATTGCCCTTCAAGTATTGATCAGCAATCAAGAAAAAGCCAAAGAATATATCACACCATTCATCAGACCTG
TAATGCAGGCTCTTCTTCATATTATAAGAGAAACAGAAAATGATGACCTTACCCATGTAATTCAGAAAATGATCTGTGAA
TATAGTGAAGAATTTACTCCTATTGCAGTAGAAATGACACAACATTTGGCAATGACATTTAACCAAGTAATCCAGATGGG
GCCAGATGAAGAAGGTAGTGATGACAAAGCAGTTACTGCTATGGGAATTCTGAATACAATTGACACACTTCTTAGTGTAG
CTGAAGATCATTAAGAGATAACCCAACAGCTCGAGGGAATCTGCTTACAGGTCGTTCCTACTGTTTTACAACAGCACGTC
TTAGAATTCCAGGAGGAGATCTTCTCTTTAGTGCACAGTTTGACATGACAACAAGTGTCTCCACAGATGTGGCAGTTACT
TCCCCTTGTATTTGAAGTCTTCCAGCAAGATGGCTTTGATTACTTTACAGATAATGATGCCCCTCCTTCATAATTATGTA
ACAGTTGATACAGACACACTTCTGTCTGACACCAAGTATCTTGAAAGATATACAGTATGTGCAAAAAGGTTCTCATAGGA
GTTGCAGGAGAAGATGTAGAGTGTCATGCAGCAACATTGTTAGAGGTCATCATTCTGCAGTGCAAAGGGTGTGGCACTGA
CCAG

Alignment

ORF - retro_pabe_1036 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.42 %
• Parental protein coverage: 59.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  INQGVSHALTWKNLKPHIQGIIQDVIFPLMCYTDADEELWQEDPYEYIRMKFDVFEDFISPTTAAQTLLF
          .NQGVSHALTWKN.KPHIQGIIQDVIFPLMCYTDADEELWQEDPYEYIRMKFDVFEDFISPTTAAQTLLF
Retrocopy LNQGVSHALTWKNPKPHIQGIIQDVIFPLMCYTDADEELWQEDPYEYIRMKFDVFEDFISPTTAAQTLLF

Parental  TACSKRKEVLQKTMGFCYQILTEPNADPRKKDGALHMIGSLAEILLKKKIYKDQMEYMLQNHVFPLFSSE
          TACSKRKEVLQKTMGFCYQILTEPNADPRKKDGALHMIGSLAEILLKKKIYKDQME.MLQNHV.PLFSSE
Retrocopy TACSKRKEVLQKTMGFCYQILTEPNADPRKKDGALHMIGSLAEILLKKKIYKDQMECMLQNHVLPLFSSE

Parental  LGYMRARACWVLHYFCEVKFKSDQNLQTALELTRRCLIDDREMPVKVEAAIALQVLISNQEKAKEYITPF
          L.YMRARACWVLHYFCEVKF.SDQNLQTALELTRRCLIDDREMPVKVEAAIALQVLISNQEKAKEYITPF
Retrocopy LRYMRARACWVLHYFCEVKFESDQNLQTALELTRRCLIDDREMPVKVEAAIALQVLISNQEKAKEYITPF

Parental  IRPVMQALLHIIRETENDDLTNVIQKMICEYSEEVTPIAVEMTQHLAMTFNQVIQTGPDEEGSDDKAVTA
          IRPVMQALLHIIRETENDDLT.VIQKMICEYSEE.TPIAVEMTQHLAMTFNQVIQ.GPDEEGSDDKAVTA
Retrocopy IRPVMQALLHIIRETENDDLTHVIQKMICEYSEEFTPIAVEMTQHLAMTFNQVIQMGPDEEGSDDKAVTA

Parental  MGILNTIDTLLSVVEDHKEITQQLEGICLQVIGTVLQQHVLEFYEEIFSLAHSLTCQQVSPQMWQLLPLV
          MGILNTIDTLLSV.EDH.EITQQLEGICLQV..TVLQQHVLEF.EEIFSL.HSLT.QQVSPQMWQLLPLV
Retrocopy MGILNTIDTLLSVAEDH*EITQQLEGICLQVVPTVLQQHVLEFQEEIFSLVHSLT*QQVSPQMWQLLPLV

Parental  FEVFQQDGFDYFTD-MMPLLHNYVTVDTDTLLSDTKYLE-MIYSMCKKVLTGVAGEDAECHAAKLLEVII
          FEVFQQDGFDYFTD.MMPLLHNYVTVDTDTLLSDTKYLE..IYSMCKKVL.GVAGED.ECHAA.LLEVII
Retrocopy FEVFQQDGFDYFTD>MMPLLHNYVTVDTDTLLSDTKYLE<KIYSMCKKVLIGVAGEDVECHAATLLEVII

Parental  LQCKGRGIDQ
          LQCKG.G.DQ
Retrocopy LQCKGCGTDQ

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	45.17 RPM
SRP007412_cerebellum	0.00 RPM	46.57 RPM
SRP007412_heart	0.00 RPM	46.51 RPM
SRP007412_kidney	0.03 RPM	37.65 RPM
SRP007412_liver	0.03 RPM	22.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1036 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1036 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1036 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_973

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015965	1 retrocopy	retro_ecab_345,
Homo sapiens	ENSG00000205339	1 retrocopy	retro_hsap_501,
Gorilla gorilla	ENSGGOG00000002260	1 retrocopy	retro_ggor_973,
Macaca mulatta	ENSMMUG00000023636	1 retrocopy	retro_mmul_437,
Pongo abelii	ENSPPYG00000029652	1 retrocopy	retro_pabe_1036 ,