RetrogeneDB ID: retro_pabe_1886

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:36036547..36036815(+)
• Located in intron of: ENSPPYG00000011856

Retrocopy information

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

Parental gene information

• Parental gene symbol: JTB
• Ensembl ID: ENSPPYG00000000791
• Aliases: None
• Description: jumping translocation breakpoint [Source:HGNC Symbol;Acc:6201]

Sequence

>retro_pabe_1886
ATCTGCATAGAAGAGGGCACTGCCCATTCTCATTTCCAGGCTAAAGTCACCCCAGAGTGTGGCTTCACAGGGTGTGTGGA
GAAAACCGCAAGCAGCTCATCTAAGGAATGAGTTTGAAAGCCTCCCGCTCGGCTCTGATGGAAATACACCTGTTCTGGAA
ATTTGAAGGGGCTGTTGATGTGGCCTTGATCTTTGCCTGTCTTGTCATCAGTTGTCAGCAACAACTGGGCAAAAAGCTCT
GGAAAAGGTCTGGAGGCAAATTGAGTCC

Alignment

ORF - retro_pabe_1886 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.44 %
• Parental protein coverage: 62.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVAEECSPCSNFRAKTTPECGSTGYVEKITCSSSKR-NEFKSCRSALMEQRLFWKFEGAVVCVALIFACL
          ...EE....S.F.AK.TPECG.TG.VEK...SSSK.....K..RSALME..LFWKFEGA.V.VALIFACL
Retrocopy ICIEEGTAHSHFQAKVTPECGFTGCVEKTASSSSKE<MSLKASRSALMEIHLFWKFEGA-VDVALIFACL

Parental  VIIRQRQLDR-KALEKVRKQIES
          VI..Q.QL...KALEKV..QIES
Retrocopy VISCQQQLGK<KALEKVWRQIES

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	22.06 RPM
SRP007412_cerebellum	0.12 RPM	32.22 RPM
SRP007412_heart	0.00 RPM	12.49 RPM
SRP007412_kidney	0.03 RPM	37.69 RPM
SRP007412_liver	0.06 RPM	41.92 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1886 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1886 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1886 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_496

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002520	1 retrocopy	retro_chof_1297,
Callithrix jacchus	ENSCJAG00000009973	1 retrocopy	retro_cjac_496,
Dasypus novemcinctus	ENSDNOG00000000740	1 retrocopy	retro_dnov_1095,
Echinops telfairi	ENSETEG00000008256	1 retrocopy	retro_etel_1340,
Felis catus	ENSFCAG00000012590	2 retrocopies	retro_fcat_1025, retro_fcat_1838,
Myotis lucifugus	ENSMLUG00000013299	1 retrocopy	retro_mluc_2225,
Oryctolagus cuniculus	ENSOCUG00000011788	1 retrocopy	retro_ocun_470,
Procavia capensis	ENSPCAG00000003210	1 retrocopy	retro_pcap_301,
Pongo abelii	ENSPPYG00000000791	1 retrocopy	retro_pabe_1886 ,
Sus scrofa	ENSSSCG00000006559	1 retrocopy	retro_sscr_687,
Tupaia belangeri	ENSTBEG00000012646	1 retrocopy	retro_tbel_762,