RetrogeneDB ID: retro_pabe_2739

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:60435769..60436016(-)
• Located in intron of: ENSPPYG00000015486

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V2
• Ensembl ID: ENSPPYG00000018575
• Aliases: None
• Description: Ubiquitin-conjugating enzyme E2 variant 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R6C9]

Sequence

>retro_pabe_2739
GGTCTTGTTAGCTGTGGCCTTGAAGGTGATGAAGAAAGACACTTTCAAGGTGGACAGGTATAATTATTGGGTCACCAAGA
ACAAATTTGAAAAACAAAATATGCCGATTGAAATTAGCATGTAGCACCTAAATATCCAGAAGCTTCTTCATTGAATACAT
TTGTAGCAAAAGTTTATGTAAACTGAATTAGTAATTCCTAGTGAAATAGTGGATGAATTGAGAATAGTGGTGTTGGTAAA
AATGGAA

Alignment

ORF - retro_pabe_2739 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.12 %
• Parental protein coverage: 56.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GTVSWGLEDDED-MTLTRWTGMIIGPPRTNYENRIYSLKVEC-GPKYPEAPPSVRFVTKINMNGINNS-S
          G.VS.GLE.DE...TL.RWTG.IIG.PRTN..N.I..LK..C..PKYPEA.....FV.K...N.I.NS.S
Retrocopy GLVSCGLEGDEE<KTLSRWTGIIIGSPRTNLKNKICRLKLAC>APKYPEASSLNTFVAKVYVN*ISNS>S

Parental  GMVDARSIPVLAKWQ
          ..VD...I.VL.K..
Retrocopy EIVDELRIVVLVKME

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	71.16 RPM
SRP007412_cerebellum	0.12 RPM	55.33 RPM
SRP007412_heart	0.06 RPM	22.85 RPM
SRP007412_kidney	0.00 RPM	30.33 RPM
SRP007412_liver	0.00 RPM	23.78 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2739 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2739 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2739 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_902
Sus scrofa	retro_sscr_524

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023218	1 retrocopy	retro_btau_902,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979, retro_mdom_736, retro_mdom_786, retro_mdom_979,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Pongo abelii	ENSPPYG00000018575	1 retrocopy	retro_pabe_2739 ,
Ictidomys tridecemlineatus	ENSSTOG00000021769	2 retrocopies	retro_itri_568, retro_itri_900,