RetrogeneDB ID: retro_pabe_450

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:147619904..147620330(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000012967
• Aliases: None
• Description: None

Sequence

>retro_pabe_450
ATGGAGGTAAAACTGATGCCCAGTGGCCCCAAGCCCGATTCCAGCTGTGGCCGTCACCGCCGGGAGCAGAGGATCATGAT
CCAAAGGAACCAGAGTAGTTCAGAAAACTGTTTATTGGTGTTCCGAGCTTTGAAACGACAGATGATAGTTTAAGAGAACA
TTTGGAAAAATGGGCACACTCACAGATTGTATGGTAATGAGACACCCCCAAAGAAAACGTTCCAGGGGGTTTGGTTTTAT
AACTTACTCTTGCGTTGAAGAGGTGGATGCAGCAACATGTGCTCAACCACACAAGTTGGTGGGCGTCTTTTGGAACCAAA
GAGAACTCTTTCTAGAGAGGAGTCAATAAAGCCTGATGCCCATCTACCAGTGAAGAAAAATTTCCTTGGTGGTATTAAAG
AAGATACAGAAGAATATAATTTGAGA

Alignment

ORF - retro_pabe_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.34 %
• Parental protein coverage: 58.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEVKPPPGRPQPDSGRRRRRR-GEEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKW-GTLTDCVVMR
          MEVK..P..P.PDS...R.RR.G.E.HDPKEPE..RKLFIG..SFETTDDSLREH.EKW.GTLTDC.VMR
Retrocopy MEVKLMPSGPKPDSSCGRHRR<GAEDHDPKEPE*FRKLFIGVPSFETTDDSLREHLEKW<GTLTDCMVMR

Parental  DPQTKRSRGFGFVTYSCVEEVDAAMCARPHK-VDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDT
          .PQ.KRSRGFGF.TYSCVEEVDAA.CA.PHK.V.GR..EPKR..SRE.S.KP.AHL.VKK.F.GGIKEDT
Retrocopy HPQRKRSRGFGFITYSCVEEVDAATCAQPHK<VGGRLLEPKRTLSREESIKPDAHLPVKKNFLGGIKEDT

Parental  EEYNLR
          EEYNLR
Retrocopy EEYNLR

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	0.06 RPM	43.29 RPM
SRP007412_cerebellum	0.00 RPM	35.51 RPM
SRP007412_heart	0.06 RPM	19.42 RPM
SRP007412_kidney	0.00 RPM	49.22 RPM
SRP007412_liver	0.00 RPM	24.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_450 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_450 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_386

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pongo abelii	ENSPPYG00000012967	1 retrocopy	retro_pabe_450 ,
Pongo abelii	ENSPPYG00000016107	1 retrocopy	retro_pabe_821,
Pongo abelii	ENSPPYG00000025850	4 retrocopies	retro_pabe_1765, retro_pabe_2285, retro_pabe_3492, retro_pabe_3835,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480, retro_tsyr_2122,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,