RetrogeneDB ID: retro_pabe_3023

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:170406509..170407852(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IGF2BP3
• Ensembl ID: ENSPPYG00000017730
• Aliases: None
• Description: insulin-like growth factor 2 mRNA binding protein 3 [Source:HGNC Symbol;Acc:28868]

Sequence

>retro_pabe_3023
GCTAGACAAGCACCAGACAAACTGAATGGATTTCAGTTAGAGAATTTCACCTTGAAAGTAGCCTATATCCCTGATGAAAT
GGCCGCCCAGCAAAACCCCTTGCTGCAGCCCCGAGGTCGCCGGGGGCTTGGGCAGAGGGGCTCCTCAAGGCAGGGGTCTC
CAGGATCCGTGTCCAAGCAGAAACCATGTGATTTGCCTCTGCGCCTGCTGGTTCCCACCCAATTTGTTAGAGCCATCTAG
GAAAACAAGGTGCCACCATTCGGAACATCGCCAAATAGACCCAGTCTAAAATCGATGTCCACCGTGAAGAAAATGCAGGG
GCTGCTGAGAAGTCCATTACTATCCTCTCGACTCCTGAAGGCACCTCTGCGGCTTGTAAGTCTCTTCTGGAGATTATGCA
TAAGGAAGCTCAAGACATAAAATTCACAGAAGAGATCCCCTTGAAGGTTTTAGCTCATAATAAATTTGTTGGTCGTCTTA
TTGGTAAAGAAGGAAGAAATCTGAAAAAAATTGAGCAAGACACAGACACTAAAATCGCGGTACCTCCATTGCAGGAATTG
ACGCTGTATAATCCAGAACACACCGTTACAGTTAAAGGCAATGTTGAGACGTGTGCCAAAGCTGAGGAAGAGGTCGTGAA
GAAAATCAGGGAGTCTTAGGAAAATGATATTGCTTCTATGAATCTTCAAGCACATTTAATTCCTGGATTAAATCTGAACG
CCTTGGGTCTGTTCCCACCCACTTCAGGGTTGCCACCTCCCACCTCAGGGTCCCCTTCAGCCACGACTCCTCCCTACCCA
CAGTCTGAGCAATTAGAAACGGAGGCTGTTCATCTGTTTATCCCGGCTCTATCATCATCTGCCATCATCGGCAAGCAGGG
CCAGCACATCAAGCAGCTTTCTCGCTTTGCTGGAGCTTCAAGTAAGATTGCTCCAGCGGAAGCACCAGATGCTAAAGTGA
GGATGGTGATTGTCACTGGACCACCAGAGGCTCACTTCAAGGCTCAGGGAAGAATTATGGAAAAATGAAAGAAGAAAACT
TTGTTAGTCCTAAAGAAGAGGTGAAACTTGAAGCTCATATCAGAGTGCCATCCTTTGCTGCTGGCAGAGTTATTGGAAAA
GGAGGCAAAACGGTGAGTGAACTTCAGAATTTGTCAAGTGCAGGAGTTTGTTGTCCCTCGTGACCAGACACCTGATGAGA
ATGACCAAGTGGTTGTCAAAATAACTGGTCACTTCTATGCTTGCCAGGTTGCCCAGAGAAAAATTCAGGAAATTGTGACT
CAGGTAAAGCAGCACCAACAACAGAAGGCTCTGCAAAGTGGACCACCTCAGTCAAGACGGAAG

Alignment

ORF - retro_pabe_3023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.8 %
• Parental protein coverage: 77.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ARQALDKLNGFQLENFTLKVAYIPDEMAAQQNPLQQPRGRRGLGQRGSSRQGSPGSVSKQKPCDLPLRLL
          ARQA.DKLNGFQLENFTLKVAYIPDEMAAQQNPL.QPRGRRGLGQRGSSRQGSPGSVSKQKPCDLPLRLL
Retrocopy ARQAPDKLNGFQLENFTLKVAYIPDEMAAQQNPLLQPRGRRGLGQRGSSRQGSPGSVSKQKPCDLPLRLL

Parental  VPTQFVGAI-IGKEGATIRNITKQTQSKIDVHRKENAGAAEKSITILSTPEGTSAACKSILEIMHKEAQD
          VPTQFV.AI..GK.GATIRNI.K.TQSKIDVHR.ENAGAAEKSITILSTPEGTSAACKS.LEIMHKEAQD
Retrocopy VPTQFVRAI<LGKQGATIRNIAK*TQSKIDVHREENAGAAEKSITILSTPEGTSAACKSLLEIMHKEAQD

Parental  IKFTEEIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQELTLYNPERTITVKGNVETCAKAE
          IKFTEEIPLK.LAHN.FVGRLIGKEGRNLKKIEQDTDTKI...PLQELTLYNPE.T.TVKGNVETCAKAE
Retrocopy IKFTEEIPLKVLAHNKFVGRLIGKEGRNLKKIEQDTDTKIAVPPLQELTLYNPEHTVTVKGNVETCAKAE

Parental  EEIMKKIRESYENDIASMNLQAHLIPGLNLNALGLFPPTSGMPPPTSGPPSAMTPPYPQFEQSETETVHL
          EE..KKIRES.ENDIASMNLQAHLIPGLNLNALGLFPPTSG.PPPTSG.PSA.TPPYPQ.EQ.ETE.VHL
Retrocopy EEVVKKIRES*ENDIASMNLQAHLIPGLNLNALGLFPPTSGLPPPTSGSPSATTPPYPQSEQLETEAVHL

Parental  FIPALSVGAIIGKQGQHIKQLSRFAGASIKIAPAEAPDAKVRMVIITGPPEAQFKAQGRI-YGKIKEENF
          FIPALS..AIIGKQGQHIKQLSRFAGAS.KIAPAEAPDAKVRMVI.TGPPEA.FKAQGRI.YGK.KEENF
Retrocopy FIPALSSSAIIGKQGQHIKQLSRFAGASSKIAPAEAPDAKVRMVIVTGPPEAHFKAQGRI<YGKMKEENF

Parental  VSPKEEVKLEAHIRVPSFAAGRVIGKGGKTVNELQNLSSA-EVVVPRDQTPDENDQVVVKITGHFYACQV
          VSPKEEVKLEAHIRVPSFAAGRVIGKGGKTV.ELQNLSSA.E.VVPRDQTPDENDQVVVKITGHFYACQV
Retrocopy VSPKEEVKLEAHIRVPSFAAGRVIGKGGKTVSELQNLSSA>EFVVPRDQTPDENDQVVVKITGHFYACQV

Parental  AQRKIQEILTQVKQHQQQKALQSGPPQSRRK
          AQRKIQEI.TQVKQHQQQKALQSGPPQSRRK
Retrocopy AQRKIQEIVTQVKQHQQQKALQSGPPQSRRK

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	0.11 RPM
SRP007412_cerebellum	0.00 RPM	0.49 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.20 RPM
SRP007412_liver	0.00 RPM	0.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3023 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3023 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3690
Gorilla gorilla	retro_ggor_2495

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002341	1 retrocopy	retro_chof_828,
Homo sapiens	ENSG00000136231	1 retrocopy	retro_hsap_3690,
Gorilla gorilla	ENSGGOG00000010286	1 retrocopy	retro_ggor_2520,
Nomascus leucogenys	ENSNLEG00000014780	1 retrocopy	retro_nleu_2277,
Pongo abelii	ENSPPYG00000014373	3 retrocopies	retro_pabe_1723, retro_pabe_281, retro_pabe_837,
Pongo abelii	ENSPPYG00000017730	1 retrocopy	retro_pabe_3023 ,