RetrogeneDB ID: retro_pabe_1803

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:10535024..10535335(-)
• Located in intron of: ENSPPYG00000010718

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSA
• Ensembl ID: ENSPPYG00000000893
• Aliases: None
• Description: endosulfine alpha [Source:HGNC Symbol;Acc:3360]

Sequence

>retro_pabe_1803
ATGTCCCAGAAACTAAACGAGAACACCTTGGAGGAGACAGGCGAGAAGCAAGACATGCAGGAGAAAGAATGTACTCTCCC
TGAAAGAGTGGAGAAGGCAAAGCTAAAGGCCAAATATCCAAGCCTACAACAAAGGCCTCGGGGCCCAGCTTCCTTATGAA
GGGACTCCGAAAAGGGAAACAGTACTTTGACTCAGGAGACTACAACATGGCCAAAGCCAAATAGGATAATAAGCAGCTGC
CAAGTGCACAACCAAACAAGAACCTGATTACTGGTGACCACATCCCCACCACACAGGATCTGCCCCAGAAA

Alignment

ORF - retro_pabe_1803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.83 %
• Parental protein coverage: 87.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQKQEEENPAEETGEEKQDTQEKEGILPERAEEAKLKAKYPSLGQKP-GGSDFLMKRLQKGQKYFDSGD
          MSQK..E.N..EETGE.KQD.QEKE..LPER.E.AKLKAKYPSL.Q.P..G..FLMK.L.KG..YFDSGD
Retrocopy MSQKLNE-NTLEETGE-KQDMQEKECTLPERVEKAKLKAKYPSLQQRP<SGPSFLMKGLRKGKQYFDSGD

Parental  YNMAKAKMKNKQLPSAGPDKNLVTGDHIPTPQDLPQR
          YNMAKAK..NKQLPSA.P.KNL.TGDHIPT.QDLPQ.
Retrocopy YNMAKAK*DNKQLPSAQPNKNLITGDHIPTTQDLPQK

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	170.02 RPM
SRP007412_cerebellum	0.00 RPM	30.77 RPM
SRP007412_heart	0.00 RPM	15.11 RPM
SRP007412_kidney	0.03 RPM	79.09 RPM
SRP007412_liver	0.00 RPM	30.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1803 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1803 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1803 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2452

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000143420	3 retrocopies	retro_hsap_1449, retro_hsap_2208, retro_hsap_2452,
Mus musculus	ENSMUSG00000038619	1 retrocopy	retro_mmus_2675,
Oryctolagus cuniculus	ENSOCUG00000003267	3 retrocopies	retro_ocun_296, retro_ocun_396, retro_ocun_722,
Otolemur garnettii	ENSOGAG00000005863	3 retrocopies	retro_ogar_1769, retro_ogar_1911, retro_ogar_2262,
Pongo abelii	ENSPPYG00000000893	2 retrocopies	retro_pabe_1803 , retro_pabe_2081,
Pongo abelii	ENSPPYG00000006487	2 retrocopies	retro_pabe_120, retro_pabe_1923,
Rattus norvegicus	ENSRNOG00000048617	1 retrocopy	retro_rnor_1776,