RetrogeneDB ID: retro_pabe_338

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:194118286..194119288(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGT1
• Ensembl ID: ENSPPYG00000020493
• Aliases: None
• Description: magnesium transporter protein 1 precursor [Source:RefSeq peptide;Acc:NP_001124931]

Sequence

>retro_pabe_338
GCAAATATGGCAGAAGTGTGGTGCCTTTGGCGTCTACTTTTGACCGTAGTGGTGGCCCTGTTATTCGTGGCTCCCGGGGT
TCCTACACATCCTTCCCGATGGAAGAAGGTGTTGGCCAAAAAGGTCAGCCAGCTGATGGATTGGACCAAGAAAGACAGAG
TGATAAGAATGAGTGACACCATGTTCTATCATTTTGTATTAGATGCACCAAAAAACTATTCTGTTATTGTGATGCTTACT
GCTCTCCACGAGTTCAGTTCATGTGTAATGTGCAAAGGTGCTGCTGAAGAATTTCAGATCTTGGCAAATTCCTATCAACG
CCCTGGTGCATTCACCACAAAGGTATTTTTTGCAATGGTGGATTATGATGAAAGCCCTGAGGTCTTTGAAGCGCTCCAGG
TAATGTCAGTTCCGAGTTTCTTCCACTTTTCTGCCCAATGGAAATTTACAACAGATGACATTTATAATTTGAGAGGAAGG
GATATTGTTGCTGACCAAATAGCTGAATGGGTAGCAGAAAGAACACATGTTAGCGTCAGAATCAGACAGCCTACAAATTA
TCATGGTCTCCTCAAGCCGGGGATACTTTTGGCTCTCATTGGTGGACTTGGGTATTTCTTGAAATGGAATAGGAAATCTA
TTTCTTGCAGAATTTTGTGCGAAGTTTTAACTCTGTGCTTTGTGATTGTGATGACGTCTGGTCAAATGTGGACTTATATA
AGAGGAGAACCGTATGTCCAAAGGGACCCTCACACAGGACATAAACATTATATCAGTAAATTTAGTCAGGCTCAGTTTGC
AGCAGAAACATTCATTATTTCCCTGTTTAATATGTGTGTTAGCCTGGGAATGGTGCTGTTAGACAAGGCTGCCACCTCTA
CGATGACCATCATAAAGAGAAAGATGATGTGTCTGGCTGGTATGTGTCTTGTTGCCATATTCTTCAGTTGGCTGCTTGCC
CTCTTTAGATTTAAAGTACCTGACTATCCATACAGCTTTGTC

Alignment

ORF - retro_pabe_338 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.98 %
• Parental protein coverage: 91.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANMAAGWWFWCVSVTVAVALLIVCD-VPSVSAQRKKEMVLSEKVSQLMEWTNKRPVIRMNGDKFRRLVKA
          ANMA..W..W....TV.VALL.V...VP......KK..VL..KVSQLM.WT.K..VIRM....F...V..
Retrocopy ANMAEVWCLWRLLLTVVVALLFVAPGVPTHPSRWKK--VLAKKVSQLMDWTKKDRVIRMSDTMFYHFVLD

Parental  PPRNYSVIVMFTALQLHRQCVVCKQADEEFQILANSWRYSSAFTNRIFFAMVDFDEGSDVFQMLNMNSAP
          .P.NYSVIVM.TAL.....CV.CK.A.EEFQILANS.....AFT...FFAMVD.DE...VF..L...S.P
Retrocopy APKNYSVIVMLTALHEFSSCVMCKGAAEEFQILANSYQRPGAFTTKVFFAMVDYDESPEVFEALQVMSVP

Parental  TFINFPAKGKPKRGDTYELQVRGFSAEQIARWIADRTDVNIRVIRPPNYAGPLMLGLLLAVIGGLVYLRR
          .F..F.A..K....D.Y.L..R...A.QIA.W.A.RT.V..R...P.NY.G.L..G.LLA.IGGL.Y...
Retrocopy SFFHFSAQWKFTTDDIYNLRGRDIVADQIAEWVAERTHVSVRIRQPTNYHGLLKPGILLALIGGLGYFLK

Parental  SNMEFLFNKTGWAFAALCFVLAMTSGQMWNHIRGPPYAHKNPHTGHVNYIHGSSQAQFVAETHIVLLFNG
          .N..............LCFV..MTSGQMW..IRG.PY....PHTGH..YI...SQAQF.AET.I..LFN.
Retrocopy WNRKSISCRILCEVLTLCFVIVMTSGQMWTYIRGEPYVQRDPHTGHKHYISKFSQAQFAAETFIISLFNM

Parental  GVTLGMVLLCEAATSDMDIGKRKIMCVAGIGLVVLFFSWMLSIFRSKYHGYPYSFL
          .V.LGMVLL..AATS.M.I.KRK.MC.AG..LV..FFSW.L..FR.K...YPYSF.
Retrocopy CVSLGMVLLDKAATSTMTIIKRKMMCLAGMCLVAIFFSWLLALFRFKVPDYPYSFV

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	0.22 RPM	5.20 RPM
SRP007412_cerebellum	0.61 RPM	7.05 RPM
SRP007412_heart	0.00 RPM	17.31 RPM
SRP007412_kidney	1.23 RPM	24.73 RPM
SRP007412_liver	0.06 RPM	28.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_338 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_338 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_377

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000010342	1 retrocopy	retro_ggor_377,
Loxodonta africana	ENSLAFG00000012886	1 retrocopy	retro_lafr_743,
Oryctolagus cuniculus	ENSOCUG00000000203	1 retrocopy	retro_ocun_1807,
Pongo abelii	ENSPPYG00000020493	1 retrocopy	retro_pabe_338 ,