RetrogeneDB ID: retro_mmul_409

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:126461272..126462690(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IGF2BP2
• Ensembl ID: ENSMMUG00000023416
• Aliases: None
• Description: None

Sequence

>retro_mmul_409
ATGATGAACAAGCTTTACATCGGGAACCTGAGCCCAGCCGTCACCGCCGACGACCTCCGGCAGCTCTTTGGGGACAGCAA
GCTGCCCCTGGCGGGACAGGTCCTGCTCAAGTCCGGCCACGCCTGTGTGGACTACCCCGACCAGAACTGGGCCATCTGTG
CCATCGAGACCGTCTCGGGTAAAGTGGAATTGCATGGGAAAATCGTGGAAGTTGATTCAGTCTCTAAAAAGCTAAGGAGC
AGGAAAATTCAGATTTGAAACATCCCTCCTCGCCTGCAGTGGGAGGTGTTGGATGGACTTTTGGCTCAATATGGAACAGT
GGAGAGTGTGGAACAAGTCAACACAGACACAGAAACCGCTATTGTCAACGTCACATATGCAACAAGAGAAGAAGCAAAAA
TAGTGATGGAGAAGCTAAGTGGGCATCAGTGTGAGAACTACTCCTTCAAGATTTCCCACATCCCGGATGAAGAGGTGAGC
TCCCCTTCACCCCCTCAGCGAGCCCAGTGTGGGGACCACTCTTCCCGGGGAGCAAGGCCAGCCCCTGGGGGCGCTTCTCA
GGCCAGACAGATTGATTTCCCACTGCGGATCCTGGTCCCCACCCAGTTTGTTGGTGCCATCATCGGAAAGGAGGGCTTGA
CCATAAAGAACATCACTAAGCAGACCCAGTCCCAGGTAGACATCCATAGAAAAGAGAACTCTGGAGCTGCAGAGAAGCCT
GTCACCATCCATGTCACCCCACGGGGGACTTCTGAAGCATGCCGCATGATTCCCGAAATCATGCAGAAAGAGGCAGATGA
GACCAAACTAGCCGAAGAGATTCCTCTGAAAATCTTGGCCCGTAATAGCTTGGTTGGAAGACTGACTGGAAAAGAAGGCA
GGAATTTGAAGAAAATTCAACATGAAACAGGGACCGAGATAGCAATCTCATCTTTGCAAGATTTGAGTATATACAATCCG
GAAAGAACCACCACTGTGAAGGGCACAGTTGAGGCCTGTGCCAGTGCTGAGATAGAGATTATGAAGAAGCTGCGTGAGGC
CTTTGAAAAGGATATGTTGGCTGTTAATACCCACTCCAGATACTTCTCCAGCCTGCACCCCCATCACCAGTTTGGCCCGT
TCTCGCATCATCACTGTTATCCAGAAGAGGAGACTGTGAATCTCTTCATCCTACCCAAGCTGTGGGCGCCATCATCGGGA
AGAAGGGGGCACACATCAAACAGCTGGTGAGATTCGCTGGAGCCTGCATCAAGATCGCCCCTGCAGAAGGCCCAGACGTC
AGCGAAAGGATGGTCATCATCACCCGGCCACCGGAAGCCCAGCTCTAGGCCCAGGGACAGATCTTTGGGAAACTGAAAGA
GGAAAACTACTTTAACCCCAAAGAAGAAGTGAAGCTGGAAGCCCATGTCAGAGTACCC

Alignment

ORF - retro_mmul_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.11 %
• Parental protein coverage: 85.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME
          MMNKLYIGNLSPAVTADDLRQLFGD.KLPLAGQVLLKSG.A.VDYPDQNWAI.AIET.SGKVELHGKI.E
Retrocopy MMNKLYIGNLSPAVTADDLRQLFGDSKLPLAGQVLLKSGHACVDYPDQNWAICAIETVSGKVELHGKIVE

Parental  VDYSVSKKLRSRKIQIRNIPPHLQWEVLDGLLAQYGTVENVEQVNTDTETAVVNVTYATREEAKIAMEKL
          VD.SVSKKLRSRKIQI.NIPP.LQWEVLDGLLAQYGTVE.VEQVNTDTETA.VNVTYATREEAKI.MEKL
Retrocopy VD-SVSKKLRSRKIQI*NIPPRLQWEVLDGLLAQYGTVESVEQVNTDTETAIVNVTYATREEAKIVMEKL

Parental  SGHQFENYSFKISYIPDEEVSSPSPPQRAQRGDHSSREQGHAPGGTSQARQIDFPLRILVPTQFVGAIIG
          SGHQ.ENYSFKIS.IPDEEVSSPSPPQRAQ.GDHSSR....APGG.SQARQIDFPLRILVPTQFVGAIIG
Retrocopy SGHQCENYSFKISHIPDEEVSSPSPPQRAQCGDHSSRGARPAPGGASQARQIDFPLRILVPTQFVGAIIG

Parental  KEGLTIKNITKQTQSRVDIHRKENSGAAEKPVTIHATPEGTSEACRMILEIMQKEADETKLAEEIPLKIL
          KEGLTIKNITKQTQS.VDIHRKENSGAAEKPVTIH.TP.GTSEACRMI.EIMQKEADETKLAEEIPLKIL
Retrocopy KEGLTIKNITKQTQSQVDIHRKENSGAAEKPVTIHVTPRGTSEACRMIPEIMQKEADETKLAEEIPLKIL

Parental  AHNGLVGRLIGKEGRNLKKIEHETGTKITISSLQDLSIYNPERTITVKGTVEACASAEIEIMKKLREAFE
          A.N.LVGRL.GKEGRNLKKI.HETGT.I.ISSLQDLSIYNPERT.TVKGTVEACASAEIEIMKKLREAFE
Retrocopy ARNSLVGRLTGKEGRNLKKIQHETGTEIAISSLQDLSIYNPERTTTVKGTVEACASAEIEIMKKLREAFE

Parental  NDMLAVNTHSGYFSSLYPHHQFGPFPHHHSYPEQEVVNLFI-PTQAVGAIIGKKGAHIKQLARFAGASIK
          .DMLAVNTHS.YFSSL.PHHQFGPF.HHH.YPE.E.VNLFI.PTQAVGAIIGKKGAHIKQL.RFAGA.IK
Retrocopy KDMLAVNTHSRYFSSLHPHHQFGPFSHHHCYPEEETVNLFI<PTQAVGAIIGKKGAHIKQLVRFAGACIK

Parental  IAPAEGPDVSERMVIITGPPEAQFKAQGRIFGKLKEENFFNPKEEVKLEAHIRVP
          IAPAEGPDVSERMVIIT.PPEAQ..AQG.IFGKLKEEN.FNPKEEVKLEAH.RVP
Retrocopy IAPAEGPDVSERMVIITRPPEAQL*AQGQIFGKLKEENYFNPKEEVKLEAHVRVP

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	0.00 RPM	0.34 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.32 RPM
SRP007412_cerebellum	0.32 RPM	4.97 RPM
SRP007412_heart	0.00 RPM	5.18 RPM
SRP007412_kidney	0.00 RPM	6.81 RPM
SRP007412_liver	0.04 RPM	0.28 RPM
SRP007412_testis	1.43 RPM	2.22 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_409 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_409 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 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,