RetrogeneDB ID: retro_ptro_635

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:91406573..91407194(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: N6AMT1
• Ensembl ID: ENSPTRG00000013817
• Aliases: None
• Description: None

Sequence

>retro_ptro_635
ATGGCAGCCCAGAGCTTCCCCATGCCATTGCACGGGCATGTGGGCTGAGGCATGTTCAGTGACATGTATGAGCCTGCGGA
GGACACGTTTCTGCTTCTGGACGCACTCCAGGTAGCGGCTGCCGAGCTGGCGGGAGTGGAAATATGCCTGGAAATAGGGG
CAGGGTCTGGTGTAGTATCTGCATTCCTAGCCTCTATGATAGGTCCTCAGGCTTTGTACATGTGCACTGATATCAACCCT
GAGGCAGCAGCTTGTACCCTAAAGACAGCATGGTGTAACAAAGTCCACATTCAACCAGTTATTACAGATGTGGTCAAATG
TTTGCTACCAATATTGAAGGAAAAAGTTGATCTTCTGGTGTTTAATCCCCTCTATGTAGTGACTCCACCTGAAGAGGTAG
GAAGTCACGGAATAGAGACAGCTTGGGCTGCTGGCAGAAATGGTCAGGAAGTCATGCACAGGTTTTTCCCCCTGGTTCCA
GATCTCCTTTCACCAAAAGGATTATTCTATTTAGTTACCATTAAAGAAAACAACCCAGGAGAAATTTGGAAAATAATGAA
GACAAAAGGTCTGCAAGGAACCACTGCACTTTCCAGACAAGCAGGCCAAGAAACTTTCAGT

Alignment

ORF - retro_ptro_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.99 %
• Parental protein coverage: 96.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGQSFATPFHGHVGRGAFSDVYEPAEDTFLLLDALEAAAAELARVEICLEVGSGSGVVSAFLASMIGPQ
          MA.QSF..P.HGHVG.G.FSD.YEPAEDTFLLLDAL..AAAELA.VEICLE.G.GSGVVSAFLASMIGPQ
Retrocopy MAAQSFPMPLHGHVG*GMFSDMYEPAEDTFLLLDALQVAAAELAGVEICLEIGAGSGVVSAFLASMIGPQ

Parental  ALYMCTDINPEAAACTLETARCNKVHIQPVITDLVKGLLPRLTEKVDLLVFNPPYVVTPPQEVGSHGIEA
          ALYMCTDINPEAAACTL.TA.CNKVHIQPVITD.VK.LLP.L.EKVDLLVFNP.YVVTPP.EVGSHGIE.
Retrocopy ALYMCTDINPEAAACTLKTAWCNKVHIQPVITDVVKCLLPILKEKVDLLVFNPLYVVTPPEEVGSHGIET

Parental  AWAGGRNGREVMDRFFPLVPDLLSPRGLFYLVTIKENNPEEILKIMKTKGLQGTTALSRQAGRETLS
          AWA.GRNG.EVM.RFFPLVPDLLSP.GLFYLVTIKENNP.EI.KIMKTKGLQGTTALSRQAG.ET.S
Retrocopy AWAAGRNGQEVMHRFFPLVPDLLSPKGLFYLVTIKENNPGEIWKIMKTKGLQGTTALSRQAGQETFS

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	1.98 RPM
SRP007412_cerebellum	0.00 RPM	1.08 RPM
SRP007412_heart	0.00 RPM	3.35 RPM
SRP007412_kidney	0.00 RPM	3.01 RPM
SRP007412_liver	0.00 RPM	0.92 RPM
SRP007412_testis	0.00 RPM	2.21 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_635 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_635 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_635 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_916
Gorilla gorilla	retro_ggor_739
Pongo abelii	retro_pabe_790

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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,