RetrogeneDB ID: retro_pabe_1723

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:22392958..22393953(+)
• 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_1723
GTCCTGCTCAAGCCCAGCTATGCCTTCGTGGACTATCCCGACCAGAACTGGGCCATCCGCGCCATCGAGACCTTCCCGGG
TCAAGTGGAATTGTATGGGAAAATCACGGAAGTTGATTACTCAGTCTCTAAAAAGCTAAGGAGCAGGAAAATTCAGATTC
GAAACATCCCTCCTCACCTCCACTGGGAGGTGTTGGATGGACTTTTGGCTCAATATGGAACTGTGGAGAATGTGGAACAA
GTCAACACAGACACAGAAACCACTGTTGTCAACGTCACATATGCAACAAGAGAAGAAAATAGCCATGCAGAAGCTAAGCG
GGCATCAGTTTGAGAACTAGCCCTTCAAGATTTCCCACATCCCAGATGAAGAGGTGAGCTCCCCTTCGCCCCCTCAGCGA
GCCCGGCGTGGGGACCACTCTTCCCAGGGAGCAAGGCCACGCCCCTGGGGGCGTTTCTCAGGCCAGACAGATTGATTTTC
TGCTGTGGATCCTGGTCCCCACCCTGTTTGTTGGTGCCATCATCAGAAAGGAGGGCTTGACCATAAAGAATATCACTAAG
CAGACCCAGTCCCAGGTAGACATCCATAGAAAAGAGAACCCTGGACCTGCAGAGAAGCCTGTCACCATCCATGCCACCCC
AGGGGGGACTTCTGAAGCATGCCACATGATTCTTGAAATCATGCAGAAAGAGGCAGATGAGAACAAACTAGCCGAAGAGA
TTCCTCTGAAAATCTTGGCCCACAATGGCTTGGTTGAAAGACTGACTGGAAAAGAAGGCAGAAATTTGAAGAAAATTGAA
CATGAAACAGGGACCAAGACAGCAATCTCATCTTTGCAGGATTTGAGCATATACAACCAGGAAAGAACCATCACTGTGAA
GGGCACAGTTGAGGCCTGTGCCAGTGCTGAGATAGAGATTATGAAGAAGCTGCGTAAGACCTTTGGAAATGATATGTTGG
CTGTTAATACGCACTCCGGATACTTCTCCAGCTTG

Alignment

ORF - retro_pabe_1723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.39 %
• Parental protein coverage: 72.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLLKSGYXXVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRSRKIQIRNIPPHLQWEVLDGLLA
          .LLK..Y..VDYPDQNWAIRAIET..G.VEL.GKI.EVDYSVSKKLRSRKIQIRNIPPHL.WEVLDGLLA
Retrocopy VLLKPSYAFVDYPDQNWAIRAIETFPGQVELYGKITEVDYSVSKKLRSRKIQIRNIPPHLHWEVLDGLLA

Parental  QYGTVENVEQVNTDTETAVVNV-TYARREEAKIAVEKLSGHQFENYSFKISYIPDEEVSSPSPPQRAQRG
          QYGTVENVEQVN..T.T....V.T.....E.KIA..KLSGHQFEN..FKIS.IPDEEVSSPSPPQRA.RG
Retrocopy QYGTVENVEQVN--TDTETTVV>TSHMQQEKKIAMQKLSGHQFEN*PFKISHIPDEEVSSPSPPQRARRG

Parental  DHSS-REQGHAPGGTSQARQIDFPLRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDIHRKENSGAAEKP
          DHSS.REQGHAPGG.SQARQIDF.L.ILVPT.FVGAII.KEGLTIKNITKQTQS.VDIHRKEN.G.AEKP
Retrocopy DHSS>REQGHAPGGVSQARQIDFLLWILVPTLFVGAIIRKEGLTIKNITKQTQSQVDIHRKENPGPAEKP

Parental  VTIHATPEGTSEACRMILEIMQKEADETKLAEEIPLKILAHNGLVGRLIGKEGRNLKKIEHETGTKITIS
          VTIHATP.GTSEAC.MILEIMQKEADE.KLAEEIPLKILAHNGLV.RL.GKEGRNLKKIEHETGTK..IS
Retrocopy VTIHATPGGTSEACHMILEIMQKEADENKLAEEIPLKILAHNGLVERLTGKEGRNLKKIEHETGTKTAIS

Parental  SLQDLSIYNPERTITVKGTVEACASAEIEIMKKLREAFENDMLAVNQQANLIPGL
          SLQDLSIYN.ERTITVKGTVEACASAEIEIMKKLR..F.NDMLAVN........L
Retrocopy SLQDLSIYNQERTITVKGTVEACASAEIEIMKKLRKTFGNDMLAVNTHSGYFSSL

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	0.12 RPM	7.42 RPM
SRP007412_heart	0.03 RPM	2.83 RPM
SRP007412_kidney	0.07 RPM	3.58 RPM
SRP007412_liver	0.06 RPM	0.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1723 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1723 has 0 orthologous retrocopies within eutheria group .

---

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,