RetrogeneDB ID: retro_pabe_3104

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:136767439..136767752(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000018050
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ERH
• Ensembl ID: ENSPPYG00000005939
• Aliases: None
• Description: enhancer of rudimentary homolog (Drosophila) [Source:HGNC Symbol;Acc:3447]

Sequence

>retro_pabe_3104
ATGTCTCACACCATTTTGCTGGTACGGACTACCAAGAGGCCAGAAGGCAGAACTTATGCTGACTACGCATCTGTGAATGA
ATGCATGGAAGGCGTTTGTAAAATGTATGAAGACGTGAAAAGAATGAATCCCAACAGTTCCTCTATCACATATGACATCA
GTCAGTTGTTTGATTTCATCAGTGATCTGGCAGGTTTACCGAGCTGCCTGGTTTACCGAGCTGATACCCAGACATACCAG
CCTTATAAAAAAAGATTGGATTAAAGAGAAGATCTACATGCTTCTTCGTTGGCAGGCTCAACAGGCTGAGAAA

Alignment

ORF - retro_pabe_3104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADL-SC
          MSHTILLV..TKRPEGRTYADY.SVNECMEGVCKMYE...KRMNPNS.SITYDISQLFDFI.DLA.L.SC
Retrocopy MSHTILLVRTTKRPEGRTYADYASVNECMEGVCKMYED-VKRMNPNSSSITYDISQLFDFISDLAGLPSC

Parental  LVYRADTQTYQPY-NKDWIKEKIYVLLRRQAQQAGK
          LVYRADTQTYQPY..KDWIKEKIY.LLR.QAQQA.K
Retrocopy LVYRADTQTYQPY>KKDWIKEKIYMLLRWQAQQAEK

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	3.26 RPM	40.75 RPM
SRP007412_cerebellum	5.72 RPM	34.29 RPM
SRP007412_heart	1.63 RPM	20.59 RPM
SRP007412_kidney	1.72 RPM	37.89 RPM
SRP007412_liver	1.87 RPM	24.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3104 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017798	4 retrocopies	retro_btau_1260, retro_btau_438, retro_btau_651, retro_btau_795,
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Erinaceus europaeus	ENSEEUG00000007758	6 retrocopies	retro_eeur_105, retro_eeur_108, retro_eeur_115, retro_eeur_116, retro_eeur_185, retro_eeur_546,
Echinops telfairi	ENSETEG00000016172	5 retrocopies	retro_etel_1122, retro_etel_1451, retro_etel_715, retro_etel_716, retro_etel_975,
Homo sapiens	ENSG00000100632	2 retrocopies	retro_hsap_3594, retro_hsap_3799,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Ochotona princeps	ENSOPRG00000000086	2 retrocopies	retro_opri_1140, retro_opri_519,
Pongo abelii	ENSPPYG00000005939	2 retrocopies	retro_pabe_2954, retro_pabe_3104 ,
Sus scrofa	ENSSSCG00000002307	1 retrocopy	retro_sscr_748,
Tursiops truncatus	ENSTTRG00000013963	2 retrocopies	retro_ttru_1671, retro_ttru_614,
Vicugna pacos	ENSVPAG00000006444	1 retrocopy	retro_vpac_423,