RetrogeneDB ID: retro_pabe_837

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:41655145..41656156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IGF2BP2
• Ensembl ID: ENSPPYG00000014373
• Aliases: None
• Description: insulin-like growth factor 2 mRNA binding protein 2 [Source:HGNC Symbol;Acc:28867]

Sequence

>retro_pabe_837
CTGGCGGGACAGGTCCTGCTCAAGTCCCGCTACGCCTTCGTAGACTACCCCGACCAGAACTGGGCCATCCGCACCAGCGA
GCCCCTCTCGGGTCAAGTGGAATTGCATGGGAAAATCATGGAAGTTGATTATTCAGTCTCTAAAAAGCTAAGGAGCAGGA
ACATTCAGATTCGAAATATCCCTCCTCACCTGCAGTGGTAGGTGTTGGATGGACTTTTGGCTCAATATGGGACAGTGGAG
AATGTGGAACAAGTCAACACAGACACAGAGACCGCTGTTGTCAACGTCACATATGCAACAAAAGAAGAAGTAAAAATCGC
CATGTAGAAGCTAAGCTGGCATCAGTTTGAGAACTACTCCTTCAAGATTTCCTACATCCCGGATGAAGAGGTGAGCTGCC
CTTCGCCCCCTCAGGGAGCCCAGCGTGGGGACCACTCTTCCTGGGAGCAAGGCCAAGCCCCTTGGGGCTCTTCTCAGGCC
AGACAGATTGATTTCCCACTGCGGATCCTGGTCCCCACCCAGTTTGTTGATGCCATCATCGGAAAGGAGGGCTTGACCAT
AAAGAACACCACTAAGCAGACCCAGTCCCAGGTAGACATCTACAGACAAGAGAACTCTGGAGCTGCAGAGAAGCCTGTCA
CCATCCATGCCACCCCAGAGGGGACTTCTGAAGCATGCCGCATGATTCTTGAAATAATGCAGAAAGAGGCAGATGAGGCC
AAACTAGCTGAAGAGATTCCTCTGGAAATCTTGGCCCACAATGGCTTGGTTGGAAGACTGATTAGAAAAGAAGGCAGAAA
TTTGAAGAAAAATGAACATGAAACAGGGACCAAGATAACAATCTCATCTTCGCAGGATTTGAGCATATACAACCCGGAAA
GAACCATCACTGTGAAGGGCACAGTCGAGGTCTGTGCCAGTGCTGAGATAGAGATTATGAGGAAGCTGCGTGAGGCCTTT
GAAAATGATATGCTGGCTGTTAATACCCACTCCAGATACTTCTCCAGCCTG

Alignment

ORF - retro_pabe_837 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.94 %
• Parental protein coverage: 72.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LANHLLLKSGYXXVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRSRKIQIRNIPPHLQWEVLD
          LA...LLKS.Y..VDYPDQNWAIR..E.LSG.VELHGKIMEVDYSVSKKLRSR.IQIRNIPPHLQW.VLD
Retrocopy LAGQVLLKSRYAFVDYPDQNWAIRTSEPLSGQVELHGKIMEVDYSVSKKLRSRNIQIRNIPPHLQW*VLD

Parental  GLLAQYGTVENVEQVNTDTETAVVNVTYARREEAKIAVEKLSGHQFENYSFKISYIPDEEVSSPSPPQRA
          GLLAQYGTVENVEQVNTDTETAVVNVTYA..EE.KIA..KLS.HQFENYSFKISYIPDEEVS.PSPPQ.A
Retrocopy GLLAQYGTVENVEQVNTDTETAVVNVTYATKEEVKIAM*KLSWHQFENYSFKISYIPDEEVSCPSPPQGA

Parental  QRGDHSSREQGHAPGGTSQARQIDFPLRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDIHRKENSGAAE
          QRGDHSS.EQG.AP.G.SQARQIDFPLRILVPTQFV.AIIGKEGLTIKN.TKQTQS.VDI.R.ENSGAAE
Retrocopy QRGDHSSWEQGQAPWGSSQARQIDFPLRILVPTQFVDAIIGKEGLTIKNTTKQTQSQVDIYRQENSGAAE

Parental  KPVTIHATPEGTSEACRMILEIMQKEADETKLAEEIPLKILAHNGLVGRLIGKEGRNLKKIEHETGTKIT
          KPVTIHATPEGTSEACRMILEIMQKEADE.KLAEEIPL.ILAHNGLVGRLI.KEGRNLKK.EHETGTKIT
Retrocopy KPVTIHATPEGTSEACRMILEIMQKEADEAKLAEEIPLEILAHNGLVGRLIRKEGRNLKKNEHETGTKIT

Parental  ISSLQDLSIYNPERTITVKGTVEACASAEIEIMKKLREAFENDMLAVNQQANLIPGL
          ISS.QDLSIYNPERTITVKGTVE.CASAEIEIM.KLREAFENDMLAVN........L
Retrocopy ISSSQDLSIYNPERTITVKGTVEVCASAEIEIMRKLREAFENDMLAVNTHSRYFSSL

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	0.50 RPM
SRP007412_cerebellum	0.24 RPM	7.42 RPM
SRP007412_heart	0.06 RPM	2.83 RPM
SRP007412_kidney	0.23 RPM	3.58 RPM
SRP007412_liver	0.00 RPM	0.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_837 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_837 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_837 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000073792	2 retrocopies	retro_hsap_216, retro_hsap_4096,
Gorilla gorilla	ENSGGOG00000015035	2 retrocopies	retro_ggor_2679, retro_ggor_2748,
Myotis lucifugus	ENSMLUG00000002631	1 retrocopy	retro_mluc_599,
Macaca mulatta	ENSMMUG00000023416	3 retrocopies	retro_mmul_2361, retro_mmul_409, retro_mmul_530,
Pongo abelii	ENSPPYG00000014373	3 retrocopies	retro_pabe_1723, retro_pabe_281, retro_pabe_837 ,
Pongo abelii	ENSPPYG00000017730	1 retrocopy	retro_pabe_3023,