RetrogeneDB ID: retro_pabe_281

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:106302779..106303769(+)
• 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_281
GCAGGACAGGTCCTGCTTAAGTCCGGCTACGTCTTCGTGGACTACCCCAAGAACCGGGCCATCCGCGCCATCGAGACCCT
CTCGGGAAAAGTGGAATTGTATGGGAAAATCATGGAAGTTGATTACTCAGTCTCTAAAAAGCTAAGGAGCAGGAAAATTC
AGATTCGAAACATCCCTCCTCACCTCCAGTGGGAGGTGTTGGATGGACTTTTGGCTCAATATGGAACAGCGGAGAATGTG
GAACAAGTCAACACAGACACAGAAACCACTGTTGTCAACGTCACATATGCAACAAGAGAAGAAAATAGACATGGAGAGGC
TAAGCAGGCATCAGTTTGAGAACTAGTCCTTCAAGATTTCCTACATCCCGGATGAAGAGGTGAGCTCCCCTTCGCCCCCT
CAGCGAGCCCAGCGTGGGGACCACTCTTCCCGGGGAGCAAGGCCACGCCCCTGGGGGCGCTTCTCAGGCCAGACAGGTTG
ATTTCCTGCTGCAGATCCTGGTCCCCACCCAGTTTGTTGGTGCCGTTATCGGAAAGGAGGGCTTGACCATAAAGAACATC
ACTAAGCAGACCCAGTGTCGGATAGACATCCATAGAAAAGAGAACTCTGGAGCTGCAGAGAAGCCTGTCACCATCCATGC
CACCCCAGGGGGGACTTCTGAAGCATGCCACATGATTCTTGAAATCATGCAGAAAGAGGCAGATGAGAACAAACTAGCCG
AAGAGATTCCTCTGAAAATCTTGGCCCACAATGGCTTGGTTGGAAAAGAAGGCAGAAATTTAAAGAAAATTGAACATGAA
ACAGGGACCAAGATAGCAATCTCGTCTTTGCAGGATTTGAGCATATACAACCAGGAAAGAACCATCACTGTGAAGGGCAC
AGTTTGAGGCCTGTGCCAGTGCTGAGATAGAGAGTATGAAGAAACTGCGTGGGACCCTTGAAAATGATATGTTGGCTGTT
AATACGCACTCCAGATACTTCTCCAGCCTG

Alignment

ORF - retro_pabe_281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.3 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ANHLLLKSGYXXVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRSRKIQIRNIPPHLQWEVLDG
          A...LLKSGY..VDYP..N.AIRAIETLSGKVEL.GKIMEVDYSVSKKLRSRKIQIRNIPPHLQWEVLDG
Retrocopy AGQVLLKSGYVFVDYP-KNRAIRAIETLSGKVELYGKIMEVDYSVSKKLRSRKIQIRNIPPHLQWEVLDG

Parental  LLAQYGTVENVEQVNTDTETAVVNV-TYARREEAKIAVEKLSGHQFENYSFKISYIPDEEVSSPSPPQRA
          LLAQYGT.ENVEQVN..T.T....V.T.....E.KI..E.LS.HQFEN.SFKISYIPDEEVSSPSPPQRA
Retrocopy LLAQYGTAENVEQVN--TDTETTVV>TSHMQQEKKIDMERLSRHQFEN*SFKISYIPDEEVSSPSPPQRA

Parental  QRGDHSSR-EQGHAPGGTSQARQIDFPLRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDIHRKENSGAA
          QRGDHSSR.EQGHAPGG.SQARQ.DF.L.ILVPTQFVGA.IGKEGLTIKNITKQTQ.R.DIHRKENSGAA
Retrocopy QRGDHSSR>EQGHAPGGASQARQVDFLLQILVPTQFVGAVIGKEGLTIKNITKQTQCRIDIHRKENSGAA

Parental  EKPVTIHATPEGTSEACRMILEIMQKEADETKLAEEIPLKILAHNGLVGRLIGKEGRNLKKIEHETGTKI
          EKPVTIHATP.GTSEAC.MILEIMQKEADE.KLAEEIPLKILAHNGLVG.....EGRNLKKIEHETGTKI
Retrocopy EKPVTIHATPGGTSEACHMILEIMQKEADENKLAEEIPLKILAHNGLVGK----EGRNLKKIEHETGTKI

Parental  TISSLQDLSIYNPERTITVKGTV-EACASAEIEIMKKLREAFENDMLAVNQQANLIPGL
          .ISSLQDLSIYN.ERTITVKGTV.EACASAEIE.MKKLR...ENDMLAVN........L
Retrocopy AISSLQDLSIYNQERTITVKGTV>EACASAEIESMKKLRGTLENDMLAVNTHSRYFSSL

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	0.00 RPM	7.42 RPM
SRP007412_heart	0.00 RPM	2.83 RPM
SRP007412_kidney	0.00 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_281 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_281 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,