RetrogeneDB ID: retro_pabe_1043

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:34241555..34241892(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAMT
• Ensembl ID: ENSPPYG00000009315
• Aliases: None
• Description: guanidinoacetate N-methyltransferase [Source:HGNC Symbol;Acc:4136]

Sequence

>retro_pabe_1043
CTGATGGAGCCTGGGGGGGGCCATTACATGCATACGCTGGTGGCTGCCACCACCTTTAAAGGGGCCTGGGTCCTGGAGGT
GGGCTTGAGTGTGGCCATTGCAGCCTTATGGTGCGGGAGGCCTCCATCAATGAACACTGGATCATCAAGTGCAGTGATGG
TGACTTCCAGCAACTCCAGGGCTTGGCCAAGCAGCAGCCATGCAAGGTTGTCCCCTTGAAAGGCCTGTGGGAGAGAGTGG
TGCCCCCTTGCTGGATGTTCACTTTGATGGGATCCTGTAGGACACATGCCCACTTTTGGAAGAGGCCTGGCACATACGCC
AGTTCAACTTCACTAAG

Alignment

ORF - retro_pabe_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.13 %
• Parental protein coverage: 56.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VMERWETPYMHALAAAASSKGGRVLEVGFGMAIAAS-KMQEGPIDEHWIIECNDGVFQRLQDWAPRQIHK
          .ME.....YMH.L.AA...KG..VLEVG...AIAA.....E..I.EHWII.C.DG.FQ.LQ..A..Q..K
Retrocopy LMEPXXXHYMHTLVAATTFKGAWVLEVGLSVAIAAL<MVREASINEHWIIKCSDGDFQQLQGLAKQQPCK

Parental  VVPLKGLWEDVAP-TLPDGHFDGILYDTYPLSEETWHTHQFNFIK
          VVPLKGLWE.V.P..L.D.HFDGIL.DT.PL.EE.WH..QFNF.K
Retrocopy VVPLKGLWERVVP<PLLDVHFDGIL*DTCPLLEEAWHIRQFNFTK

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	6.08 RPM
SRP007412_cerebellum	0.00 RPM	2.43 RPM
SRP007412_heart	0.00 RPM	7.86 RPM
SRP007412_kidney	0.00 RPM	18.33 RPM
SRP007412_liver	0.00 RPM	36.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1043 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1043 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1251
Gorilla gorilla	retro_ggor_982

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130005	1 retrocopy	retro_hsap_1251,
Gorilla gorilla	ENSGGOG00000002809	2 retrocopies	retro_ggor_1818, retro_ggor_982,
Macropus eugenii	ENSMEUG00000005126	2 retrocopies	retro_meug_1833, retro_meug_302,
Pongo abelii	ENSPPYG00000009315	2 retrocopies	retro_pabe_1043 , retro_pabe_2162,
Tursiops truncatus	ENSTTRG00000011817	1 retrocopy	retro_ttru_195,