RetrogeneDB ID: retro_pabe_997

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:46281690..46282232(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM206A
• Ensembl ID: ENSPPYG00000019483
• Aliases: FAM206A, C9orf6
• Description: Protein FAM206A [Source:UniProtKB/Swiss-Prot;Acc:Q5RFS0]

Sequence

>retro_pabe_997
GTGGCTACCGAGCGCCACACCGCAGAGCCGGTGGTGCCTTTGTTCGTGGACCAGTACTGCACTCGCTGGTACAAAGCAGA
TGTGAAAGGAAGATCTTGTGAGGACCACTGTACACCACAGCACTCTAACCAAATAGGTGTCATCTCATTGGCAGAATCTC
ATCCAGTTCTTCAAAGCGGAAAAACAATTAAAAGCATTCCCTGTCAGATCAGTACCAACTGTAGCAGACTTCAGAACAAG
GGCTCGGGGAAATGTAAGCGGGGGGCGCAGTTTCTAACAGAACTTGCACCTCTCTGTAAGATTTACTGCTCAGATGGCAA
AGAATATACTGTATCTAGTTGTGTTAGAGGATGTTCGATGAAAGTGAATGAAAAACATTCTCCATAAGCCATCTATTCTT
CAAGACAAGCCGTCCACTGAAGGCTACATTGCAGTTGTTACCCAAATTTGAAGAAAGTAAAAACATAGCGGAAGGGTTAC
TGACACAAAAACAGTATGAAGAAGTCATGGTGAAATGCATTAATGCCACAACAGCGATGTCA

Alignment

ORF - retro_pabe_997 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MATEPEAAEPVVPSLVDRYFTRWYKPDVKGKFCEDHCILQHSNRICVITLAESHPVLQSGKTIKSISYQI
          .ATE...AEPVVP..VD.Y.TRWYK.DVKG..CEDHC..QHSN.I.VI.LAESHPVLQSGKTIKSI..QI
Retrocopy VATERHTAEPVVPLFVDQYCTRWYKADVKGRSCEDHCTPQHSNQIGVISLAESHPVLQSGKTIKSIPCQI

Parental  STNCSRLQNKVSGKFKRGAQFLTELAPLCKIYCSDGEEYTVSSCVRGRLMEVNE-NILHKPSILQEKPST
          STNCSRLQNK.SGK.KRGAQFLTELAPLCKIYCSDG.EYTVSSCVRG..M.VNE.NILHKPSILQ.KPST
Retrocopy STNCSRLQNKGSGKCKRGAQFLTELAPLCKIYCSDGKEYTVSSCVRGCSMKVNE>NILHKPSILQDKPST

Parental  EGYIAVV-LPKFEESK-SITEGLLTQKQYEEVMVKRINATTATS
          EGYIAVV..P.....K..I.EGLLTQKQYEEVMVK.INATTA.S
Retrocopy EGYIAVV<YPNLKKVK<NIAEGLLTQKQYEEVMVKCINATTAMS

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	10.28 RPM
SRP007412_cerebellum	0.00 RPM	7.90 RPM
SRP007412_heart	0.00 RPM	4.76 RPM
SRP007412_kidney	0.00 RPM	8.12 RPM
SRP007412_liver	0.00 RPM	4.44 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_997 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_997 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_997 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1197

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004996	1 retrocopy	retro_btau_873,
Canis familiaris	ENSCAFG00000028510	1 retrocopy	retro_cfam_1345,
Cavia porcellus	ENSCPOG00000005927	1 retrocopy	retro_cpor_1488,
Dipodomys ordii	ENSDORG00000008618	1 retrocopy	retro_dord_611,
Homo sapiens	ENSG00000119328	1 retrocopy	retro_hsap_1197,
Macropus eugenii	ENSMEUG00000013637	1 retrocopy	retro_meug_1321,
Microcebus murinus	ENSMICG00000002074	1 retrocopy	retro_mmur_1363,
Monodelphis domestica	ENSMODG00000012563	1 retrocopy	retro_mdom_1837,
Oryctolagus cuniculus	ENSOCUG00000001882	1 retrocopy	retro_ocun_1527,
Otolemur garnettii	ENSOGAG00000024317	1 retrocopy	retro_ogar_1200,
Pongo abelii	ENSPPYG00000019483	1 retrocopy	retro_pabe_997 ,
Sorex araneus	ENSSARG00000009305	1 retrocopy	retro_sara_313,
Ictidomys tridecemlineatus	ENSSTOG00000027231	1 retrocopy	retro_itri_583,