RetrogeneDB ID: retro_pabe_2162

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:124228063..124228388(-)
• 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_2162
GAGCGCCCCTACTGCAACCCCCTTCACTGCCTTCACCACCTCCAAAGGGGGCCGAGTCTTAGAGGTGGGCTTCGGCATGG
CCACAAGAACATGGAAGGTGCAGGAGGTCGCCATCCAGGAACACTGGATCATGGAGTGCAATGACAGCATCTTCCAGCTG
CTCCAGGACTGGACCCAGCAGCAGCCACACAAGGTCATCCCCTTGAAAGTCCTGTGGAAGGAGGTGGCGCTCACCCTGCC
AGGTGGTCGCTTTGATGGGATCCTGTATGACACGTACCCACTGTAGGAAGAGACCTGGCACACACACCAGCTCAACTTCA
TCGAG

Alignment

ORF - retro_pabe_2162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.89 %
• Parental protein coverage: 54.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETPYMHAL-AAAASSKGGRVLEVGFGMAIAASKMQEGPIDEHWIIECNDGVFQRLQDWAPRQIHKVVPLK
          E.PY...L..A...SKGGRVLEVGFGMA....K.QE..I.EHWI.ECND..FQ.LQDW...Q.HKV.PLK
Retrocopy ERPYCNPL>TAFTTSKGGRVLEVGFGMATRTWKVQEVAIQEHWIMECNDSIFQLLQDWTQQQPHKVIPLK

Parental  GLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIK
          .LW..VA.TLP.G.FDGILYDTYPL.EETWHTHQ.NFI.
Retrocopy VLWKEVALTLPGGRFDGILYDTYPL*EETWHTHQLNFIE

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	0.24 RPM	2.43 RPM
SRP007412_heart	0.00 RPM	7.86 RPM
SRP007412_kidney	0.03 RPM	18.33 RPM
SRP007412_liver	0.03 RPM	36.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2162 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2162 has 0 orthologous retrocopies within eutheria group .

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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,