RetrogeneDB ID: retro_pabe_1937

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:28922430..28922944(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP4A
• Ensembl ID: ENSPPYG00000005691
• Aliases: None
• Description: charged multivesicular body protein 4A [Source:HGNC Symbol;Acc:20274]

Sequence

>retro_pabe_1937
GAGAACAGACTATCAAAGAACCATGGTTCCAAGAATAGGAGAGCTGCTCTGCAGGCTTTACAAGGGAAGAAAAGATGGGA
ACAGCAGCTGGCACAAACTGATGGAACATTATCCACCCTAGAGTTTCAGCATGAAGCCATTGAGAATGCCATTACCAATG
CAAAAATGCTTTGTACCTTGTAGTTAGCTGCGTGAGGCATGAAGAAGGCCTACCAGGACCTGGACACTGGCAAGATAGAT
GAACTGATGGATGACATCACAGAATAGCAGGAGGTGGCCCAGCAGATCTCAGATGCCATTTCTTGACCTGTGGGTTTTGG
AGAAGATGTGGGTGATCATGAACTGTTGGGGGAACTAGAGAAGCTGGAGGAGGAATTGGCCCAAGAATTGTTAAATGTGG
GGCAACAAGGAGGAAGTGAACCCCAGTCAAATGGCTAGTGTATCCTCTACACTATCTGCCTTCCTGGGAGGGTCGGCTCC
CAAAGCAGATGAAGACAAAGAAGCACTAAAGCAG

Alignment

ORF - retro_pabe_1937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.07 %
• Parental protein coverage: 66.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELQTAKKYGTKNKRAALQALRRKKRFEQQLAQTDGTLSTLEFQREAIENATTNAEVLRTMELAAQSMKKA
          E....K..G.KN.RAALQAL..KKR.EQQLAQTDGTLSTLEFQ.EAIENA.TNA..L.T..LAA..MKKA
Retrocopy ENRLSKNHGSKNRRAALQALQGKKRWEQQLAQTDGTLSTLEFQHEAIENAITNAKMLCTL*LAA*GMKKA

Parental  YQDMDIDKVDELMTDHNQQGDWPSQISDAISPAXWAFGDDVDQDELLEELEELEQEELAQELLNV-GDKE
          YQD.D..K.DELM.D.........QISDAIS.....FG.DV...ELL.ELE.LE.EELAQELLNV.G.KE
Retrocopy YQDLDTGKIDELMDDITE*QEVAQQISDAIS*PV-GFGEDVGDHELLGELEKLE-EELAQELLNV>GNKE

Parental  EEPPVKLPSVPS--AHLPAGPVPKQDEDEEALKQ
          E..P....SV.S.......G..PK.DED.EALKQ
Retrocopy EVNPSQMASVSSTLSAFLGGSAPKADEDKEALKQ

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	15.76 RPM
SRP007412_cerebellum	0.00 RPM	12.28 RPM
SRP007412_heart	0.00 RPM	6.20 RPM
SRP007412_kidney	0.00 RPM	28.24 RPM
SRP007412_liver	0.00 RPM	14.29 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1937 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1937 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1937 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2284
Gorilla gorilla	retro_ggor_1697
Macaca mulatta	retro_mmul_1035

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000254505	1 retrocopy	retro_hsap_2284,
Gorilla gorilla	ENSGGOG00000016091	1 retrocopy	retro_ggor_1697,
Microcebus murinus	ENSMICG00000001732	1 retrocopy	retro_mmur_1101,
Macaca mulatta	ENSMMUG00000012476	2 retrocopies	retro_mmul_1035, retro_mmul_1694,
Pongo abelii	ENSPPYG00000005691	1 retrocopy	retro_pabe_1937 ,
Pongo abelii	ENSPPYG00000010931	1 retrocopy	retro_pabe_1111,
Sorex araneus	ENSSARG00000008328	1 retrocopy	retro_sara_530,