RetrogeneDB ID: retro_pabe_790

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:89517181..89517802(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: N6AMT1
• Ensembl ID: ENSPPYG00000011314
• Aliases: None
• Description: N-6 adenine-specific DNA methyltransferase 1 (putative) [Source:HGNC Symbol;Acc:16021]

Sequence

>retro_pabe_790
ATGGCAGCCCAGAGCTTCCCCACGCCATTGCACGGGCATGTGGGCTGCGGCACGTTCAGTGACGTGTATGAGCCCGCGGA
GGACATGTTTCTGCTTCTGGACGCACTCCAGGTAGCGGCTGCCGAGCTGGCGGGAGTGGAAATATGCCTGGAAGTAGGGG
CAGGGTCTGGTGTAGTATCTGCATTCCTAGCCTCTATGATAGGTCCTCAGGCTTTGTACATGTGCACTGATATCAACCCT
GAGGCAGCAGCTTGTACCCTAAAGACAGCACGGTGTAACAAAGTCCACATTCAACCAGTTATTACAGATTTGGTCAAAGG
CTTGCTACCAATATTGAAGGAAAAAGTTGATCTTCTGGTGTTTAATTCCCCCTATGTAGTGACTCCACCCGAAGAGGTAG
GAAGTCACGGAATAGAGGCAGCTTGGGCTGCTGGCAGAAATGGTCAGGAAGTCATGCACAGGTTTTTCCCCCTGGTTCCA
GATATCCTTTCACCAAAAGGATTATTCTGTTTAGTTACCATTAAAGAAAACAACGCAGAAGAAATTTGGAACATAATGAA
GACCAAAGGTCTGCAAGGAACCACTGCACTTTCCAGACAAGCAGGCCAAGAAACTTTCAGT

Alignment

ORF - retro_pabe_790 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.37 %
• Parental protein coverage: 96.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGQSFPTPLHGHVGRGAFSDVYEPAEDTFLLLDALEAAAAELAGVEICLEVGSGSGVVSAFLASMIGPQ
          MA.QSFPTPLHGHVG.G.FSDVYEPAED.FLLLDAL..AAAELAGVEICLEVG.GSGVVSAFLASMIGPQ
Retrocopy MAAQSFPTPLHGHVGCGTFSDVYEPAEDMFLLLDALQVAAAELAGVEICLEVGAGSGVVSAFLASMIGPQ

Parental  ALYMCTDINPEAAACTLETARCNKVYIQPVITDLVKGLLPRLKEKVDLLVFNPPYVVTPPQEVGSHGIEA
          ALYMCTDINPEAAACTL.TARCNKV.IQPVITDLVKGLLP.LKEKVDLLVFN.PYVVTPP.EVGSHGIEA
Retrocopy ALYMCTDINPEAAACTLKTARCNKVHIQPVITDLVKGLLPILKEKVDLLVFNSPYVVTPPEEVGSHGIEA

Parental  AWAGGRNGREVMDRFFPLVPDLLSPRGLFYLVTIKENNPEEILKIMKTKGLQGTTALSRQAGQETLS
          AWA.GRNG.EVM.RFFPLVPD.LSP.GLF.LVTIKENN.EEI..IMKTKGLQGTTALSRQAGQET.S
Retrocopy AWAAGRNGQEVMHRFFPLVPDILSPKGLFCLVTIKENNAEEIWNIMKTKGLQGTTALSRQAGQETFS

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	1.49 RPM
SRP007412_cerebellum	0.00 RPM	5.23 RPM
SRP007412_heart	0.00 RPM	3.13 RPM
SRP007412_kidney	0.00 RPM	3.81 RPM
SRP007412_liver	0.00 RPM	1.32 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_790 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_790 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_790 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_916
Pan troglodytes	retro_ptro_635
Gorilla gorilla	retro_ggor_739

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005227	1 retrocopy	retro_chof_1139,
Homo sapiens	ENSG00000156239	1 retrocopy	retro_hsap_916,
Gorilla gorilla	ENSGGOG00000022382	1 retrocopy	retro_ggor_739,
Nomascus leucogenys	ENSNLEG00000002845	1 retrocopy	retro_nleu_282,
Oryctolagus cuniculus	ENSOCUG00000001084	1 retrocopy	retro_ocun_521,
Ochotona princeps	ENSOPRG00000001551	3 retrocopies	retro_opri_200, retro_opri_867, retro_opri_925,
Pongo abelii	ENSPPYG00000011314	1 retrocopy	retro_pabe_790 ,
Pan troglodytes	ENSPTRG00000013817	1 retrocopy	retro_ptro_635,
Pteropus vampyrus	ENSPVAG00000012777	2 retrocopies	retro_pvam_1166, retro_pvam_1200,
Sus scrofa	ENSSSCG00000026046	1 retrocopy	retro_sscr_130,
Ictidomys tridecemlineatus	ENSSTOG00000021743	1 retrocopy	retro_itri_497,
Tupaia belangeri	ENSTBEG00000001269	1 retrocopy	retro_tbel_777,