RetrogeneDB ID: retro_hsap_216

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:146522378..146524040(+)
• Located in intron of: ENSG00000227242

Retrocopy information

• Ensembl ID: ENSG00000225603
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IGF2BP2
• Ensembl ID: ENSG00000073792
• Aliases: IGF2BP2, IMP-2, IMP2, VICKZ2, p62
• Description: insulin-like growth factor 2 mRNA binding protein 2 [Source:HGNC Symbol;Acc:28867]

Sequence

>retro_hsap_216
GTGATGAACAATCTTTACATCGGGAACCTTAGCCCTGCGGTCACCGCCGACGACCTCTGGCAGCTCTTTGGGGACAGGAA
GCTGCCCCCCACCGGACAGGTCCTGCTCAAGTCCGGCTATGCCTTCGTGGACTACCCCTACAAGAACTGGGCCATCCGCG
CCATCGAGACCCTCTCGGGTAAAGTGGAATTGCATGGGAAAATCATGGAAGTTGATTACTCAGTCTCTAAAAAGCTAAGG
AGGAGAAAAATTCAGATTCGAAACATCCCTCCTCACCTCCAGTGGGAGGTGTTGGATGGACTTTTGGCTCAATATGGAAC
AGTGGAGAATGTGGAACAACAAGTCAACACAGACACAGAAACCACTGTTGTCAACGTCACATATGCAACAAGAGAAGAAA
ATAGACATGGAGAGGCTAAGCGGGCATCAGTTTGAGAACTAGTCCTTCAAGATTTCCTACATCCCGGATGAAGAGGTGAG
CTCCCCTTCGCCCCCTCAGCGAGCCCAGCGTGGGGACCACTCTTCCCGGGGAGCAAGGCCACGACCCTGGGGGCGCTTCT
TAGGCCAGACAGATTGATTTCCTGCTGCAGGTCCTGGTCCCCTACAGTTTGCAGTTTGTTGGTGCCATCATCAGAAAGGA
GGGCTTGACCATAAAGAACATCACTAAGTAGACCCAGTCCCGGATAGATATCCATAGAAAAGAGAACTCTGGAGCTGCAG
AGAAGCCTGTCACCATCCATGCCACCCCAGGGGGGACTTCTGAAGCATGCCTCATGATTCTTGAAATCATGCAGAAAGAG
GCAGATGAGAACAAACTAGCCGAAGAGATTCCTCTGAAAATCTTGGCCCACAATGGCTTGGTTGGAAAAGAAGGCAGAAA
TTTGAAGAAAATTGAACATGAAACAGGGACCAAGATAGCAATCTCATCTTTGCAGGATTTGAGCATAAATAACCAGGAAA
GAATCATCACTGTGAAGGGCACAGTTTGAGGCCTGTGCCAGTGCTGAGATAGAGATTATGAAGAAGCTGCGTGAGACCTT
TGAAAATGATATGTTGGCTGTTAATACGCACTCCGGATACTTCTCCAGCTTGTACCCCCATCACCAGGTTGGCCCGTTCC
CGCATCATCACTCTTATCCAGAGCAGGAGGTTGTGAATCTCTTCATCCCAACCCAGGCTGTGGGCGCCATTATCAGGAAG
AGGGGAGCACACATCAAACAGCTGGCGAGATTCGCCACAGCCTCCATCAAGATCGCCCTTGCGGAAGGCCCAGACGTCAA
CGAAAGGATGGTCATCATCACCCGGCCACCGGAAGCCCAGTTCAAGGCCCAGGGACGGATCTTTGGGAAACTGAAAGAAG
AAAACTTCTTTAACCCCAAAGAAGAAGTGAAGCTGGAAGCCCGTATCAGAGTGCCCTCTTCCACAGCTGGCCGGGTGATT
GGCAAAGGTGTCAATACCTTGAATGAACTGCAGAACTTAACCAGTGCAGAAGTCATCGTGCCTCGTGACCAAAGGCCAGA
TGAAAATGAGGAAGTGATCGTCAGAATTATTGGACACTTCTTTGCTACCCCAACTGCATAGCACAAGATCAGGGAAACTG
TACAACAGGTGAAGCAGCAAGAGCAGAAATACCCTCAGGGAGTCGCCTCACAGCACAGCAAG

Alignment

ORF - retro_hsap_216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME
          .MN.LYIGNLSPAVTADDL.QLFGDRKLP..GQVLLKSGYAFVDYP..NWAIRAIETLSGKVELHGKIME
Retrocopy VMNNLYIGNLSPAVTADDLWQLFGDRKLPPTGQVLLKSGYAFVDYPYKNWAIRAIETLSGKVELHGKIME

Parental  VDYSVSKKLRSRKIQIRNIPPHLQWEVLDGLLAQYGTVENVEQV-NTDTETAVVNVTYATREEAKIAMEK
          VDYSVSKKLR.RKIQIRNIPPHLQWEVLDGLLAQYGTVENVEQ...T.T.............E.KI.ME.
Retrocopy VDYSVSKKLRRRKIQIRNIPPHLQWEVLDGLLAQYGTVENVEQQ>STQTQKPLLSTSHM-QQEKKIDMER

Parental  LSGHQFENYSFKISYIPDEEVSSPSPPQRAQRGDHSSR-EQGHAPGGTSQARQIDFPLRILVP--TQFVG
          LSGHQFEN.SFKISYIPDEEVSSPSPPQRAQRGDHSSR.EQGH.PGG.S.ARQIDF.L..LVP...QFVG
Retrocopy LSGHQFEN*SFKISYIPDEEVSSPSPPQRAQRGDHSSR>EQGHDPGGAS*ARQIDFLLQVLVPYSLQFVG

Parental  AIIGKEGLTIKNITKQTQSRVDIHRKENSGAAEKPVTIHATPEGTSEACRMILEIMQKEADETKLAEEIP
          AII.KEGLTIKNITK.TQSR.DIHRKENSGAAEKPVTIHATP.GTSEAC.MILEIMQKEADE.KLAEEIP
Retrocopy AIIRKEGLTIKNITK*TQSRIDIHRKENSGAAEKPVTIHATPGGTSEACLMILEIMQKEADENKLAEEIP

Parental  LKILAHNGLVGRLIGKEGRNLKKIEHETGTKITISSLQDLSIYNPERTITVKGTV-EACASAEIEIMKKL
          LKILAHNG....L.GKEGRNLKKIEHETGTKI.ISSLQDLSI.N.ER.ITVKGTV.EACASAEIEIMKKL
Retrocopy LKILAHNG----LVGKEGRNLKKIEHETGTKIAISSLQDLSINNQERIITVKGTV>EACASAEIEIMKKL

Parental  REAFENDMLAVNTHSGYFSSLYPHHQFGPFPHHHSYPEQEIVNLFIPTQAVGAIIGKKGAHIKQLARFAG
          RE.FENDMLAVNTHSGYFSSLYPHHQ.GPFPHHHSYPEQE.VNLFIPTQAVGAII.K.GAHIKQLARFA.
Retrocopy RETFENDMLAVNTHSGYFSSLYPHHQVGPFPHHHSYPEQEVVNLFIPTQAVGAIIRKRGAHIKQLARFAT

Parental  ASIKIAPAEGPDVSERMVIITGPPEAQFKAQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKG
          ASIKIA.AEGPDV.ERMVIIT.PPEAQFKAQGRIFGKLKEENFFNPKEEVKLEA.IRVPSSTAGRVIGKG
Retrocopy ASIKIALAEGPDVNERMVIITRPPEAQFKAQGRIFGKLKEENFFNPKEEVKLEARIRVPSSTAGRVIGKG

Parental  GKTVNELQNLTSAEVIVPRDQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQVKQQEQKYPQGVASQRS
          ..T.NELQNLTSAEVIVPRDQ.PDENEEVIVRIIGHFFA..TA..KIRE.VQQVKQQEQKYPQGVASQ.S
Retrocopy VNTLNELQNLTSAEVIVPRDQRPDENEEVIVRIIGHFFATPTA*HKIRETVQQVKQQEQKYPQGVASQHS

Parental  K
          K
Retrocopy K

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
bodymap2_adipose	0.00 RPM	28.41 RPM
bodymap2_adrenal	0.00 RPM	4.30 RPM
bodymap2_brain	0.02 RPM	0.38 RPM
bodymap2_breast	0.08 RPM	5.84 RPM
bodymap2_colon	0.00 RPM	17.25 RPM
bodymap2_heart	0.00 RPM	19.86 RPM
bodymap2_kidney	0.00 RPM	17.16 RPM
bodymap2_liver	0.06 RPM	1.86 RPM
bodymap2_lung	0.42 RPM	56.10 RPM
bodymap2_lymph_node	0.00 RPM	10.84 RPM
bodymap2_ovary	0.00 RPM	8.67 RPM
bodymap2_prostate	0.00 RPM	7.62 RPM
bodymap2_skeletal_muscle	0.00 RPM	2.46 RPM
bodymap2_testis	0.09 RPM	18.99 RPM
bodymap2_thyroid	0.00 RPM	12.30 RPM
bodymap2_white_blood_cells	0.00 RPM	7.80 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_216 was not detected

EST

No EST(s) were mapped for retro_hsap_216 retrocopy.

TSS

No TSS is located nearby retro_hsap_216 retrocopy 5' end.

Lab

retro_hsap_216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_216 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,
Homo sapiens	ENSG00000136231	1 retrocopy	retro_hsap_3690,
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,