RetrogeneDB ID: retro_ggor_377

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:37322101..37323103(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGT1
• Ensembl ID: ENSGGOG00000010342
• Aliases: None
• Description: None

Sequence

>retro_ggor_377
GCAAATATGGCAGAAGTGTGGTGGCTTTGGCGTCTACTTTTGACCATAGTGGTGGCCCTGTTATTCGTGGCTCCCGGGGT
TCCTACACATCCTTCCTGATGGAAGAAGGCGTTGGCCAAAAAGGTCAGCCAGCTGATGGATTGGACCAAGAAAGACAGAG
TGATAAGAATGAGTGACACCATGTTCTATCATTTTGTATTAGATGCACCAAAAAACTATTCTGTTATTGTGATGCTTACT
GCTCTCCACGAGTTCAGTTCATGTGTCATGTGCAAAGGTGCTGCTGAGGAATTTCAGATCTTGGCAAATTCCTATCAACG
CCCTGGTGCATTCACCACAAAGGTATTTTTTGCAATGGTGGATTATGATGAAAGCCCTGAGGTCTTTGAAGCACTCCAGG
TAACGTCAGTTCCGACTTTCTTCCACTTTTCTGCCCAATGGAAATTTGCAACAGATGACATTTATAATTTGAGAGGAAGG
GATATTGTTGCTGACCAAATGGCTGAATGGGTAGCAGAAAGAACACATGTCAGCGTCAGAATCAGACAGCCTGCAAATTA
TCATGGTCTCCTCAAGCCAGGGATACTTCTGGCTCTCATTGGTGGACTTGGGTATTTCTTGAAATGGAATAGGAAATCTA
TTTCTTGCAGAATTTTGTGCGAAGTTTTAACTCTGTGCTTTGTGATTGTGATGACGTCTGGTCAAATGTGGACTTATGTA
AGAGGAGAACCATATGTCCAGAGGGACCCTCACACAGGACATAAACATTACATCAGTAAATTTAGTCAGGCTCAGTTTGC
AGCAGAAACATTCATTATTTCCCTGTTTAATATGTGTGTTAGTCTGGGAATGGTGCTGTTAGACAAGGCTGCCACCTCTA
CGATGAACATCATAAAGAGAAAGATGATGTGTCTGGCTGGTATGTGTCTTGTTGCCATATTCTTCAGTTGGCTGTTTTCC
CTCTTTAGATTTAAAGTACCTGACTATCCATACAGCTTTGTC

Alignment

ORF - retro_ggor_377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.08 %
• Parental protein coverage: 91.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANMAARWRFWCVSVTMAVALLIVCD-VPSASAQRKKEMVLSEKVSQLMEWTNKRPVIRMNGDKFRRLVKA
          ANMA..W..W....T..VALL.V...VP......KK...L..KVSQLM.WT.K..VIRM....F...V..
Retrocopy ANMAEVWWLWRLLLTIVVALLFVAPGVPTHPS*WKK--ALAKKVSQLMDWTKKDRVIRMSDTMFYHFVLD

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

Parental  TFINFPAKGKPKRGDTYELQVRGFSAEQIARWIADRTDVNIRVIRPPNYAGPLMLGLLLAVIGGLVYLRR
          TF..F.A..K....D.Y.L..R...A.Q.A.W.A.RT.V..R...P.NY.G.L..G.LLA.IGGL.Y...
Retrocopy TFFHFSAQWKFATDDIYNLRGRDIVADQMAEWVAERTHVSVRIRQPANYHGLLKPGILLALIGGLGYFLK

Parental  SNMEFLFNKTGWAFAALCFVLAMTSGQMWNHIRGPPYAHKNPHTGHVNYIHGSSQAQFVAETHIVLLFNG
          .N..............LCFV..MTSGQMW...RG.PY....PHTGH..YI...SQAQF.AET.I..LFN.
Retrocopy WNRKSISCRILCEVLTLCFVIVMTSGQMWTYVRGEPYVQRDPHTGHKHYISKFSQAQFAAETFIISLFNM

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

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	0.34 RPM	6.14 RPM
SRP007412_cerebellum	0.16 RPM	4.53 RPM
SRP007412_heart	0.03 RPM	3.00 RPM
SRP007412_kidney	0.61 RPM	26.01 RPM
SRP007412_liver	0.13 RPM	19.18 RPM
SRP007412_testis	17.30 RPM	19.68 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_377 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_377 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_338

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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,