RetrogeneDB ID: retro_pabe_1849

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:13454936..13455599(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GXYLT1
• Ensembl ID: ENSPPYG00000004419
• Aliases: None
• Description: glucoside xylosyltransferase 1 [Source:HGNC Symbol;Acc:27482]

Sequence

>retro_pabe_1849
ACACTAATAGCCTTTTTACGACCAGTTGATCATATTTGTTCTTTACTAAAGAAATTTAATTCCACATAAATTGCTGCAGT
GGCCTCAGAACACAAGCAACCTCAAATAAGATGGTATAGTTGCTTCTCTAGGCAACCATACTGTGGAAAAACTGGAGTAA
ACCCTGGAGTTACGTTGAGGAATATGACTCGAATGAGAAGGAAGTATTTCAAGAATGATATGACAACTGTGTGACTACAA
TGAGGAGATATACTTATGACATGGCTTAAAGAATACAAACTAAACATTACATGGGCAATCAATATTTGTTGGATATCATG
TTTTTTCACAATCCAGAAAGTCCTTTTGCCTTTCCGTGTCAATGGAATTATCGTCCAGGTCATTGTCTATATGGAAGCAG
TTGCCAAGAAGCAGAAGAAGGAATCCTGATTCTTCAGCGAACAGACGTGTTTACCATGATGATAAGCAACCAGCATTTAG
AGCTGTTTATGAAGCACTGAGAAATTGTTCTTTTAAGACGACAATGCTCATTCCCTAATGAAACCTTTAGAACTGGAACT
ACAACAAACAGTGCATACATACCGTGGAAAAATTTACAAAATATTTGTCAAACAACTAGCAAAAAGCATAAGAGATCGTT
ATGCCAGATCACCAAAGGAAAGG

Alignment

ORF - retro_pabe_1849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.32 %
• Parental protein coverage: 51.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TDILFLRPVDDIWSLLKKFNSTQIAAMAPEHEEPRIGWYNRFARHPYYGKTGVNSGVMLMNMTRMRRKYF
          T.I.FLRPVD.I.SLLKKFNST.IAA.A.EH..P.I.WY..F.R.PY.GKTGVN.GV.L.NMTRMRRKYF
Retrocopy TLIAFLRPVDHICSLLKKFNST*IAAVASEHKQPQIRWYSCFSRQPYCGKTGVNPGVTLRNMTRMRRKYF

Parental  KNDMTTVRLQWGDILMPLLKKYKLNITW-GDQDLLNIMFFHNPESLFVFPCQWNYRPDHCIYGSNCQEAE
          KNDMTTV.LQ.GDILM..LK.YKLNITW.G.Q.LL.IMFFHNPES.F.FPCQWNYRP.HC.YGS.CQEA.
Retrocopy KNDMTTV*LQ*GDILMTWLKEYKLNITW<GNQYLLDIMFFHNPESPFAFPCQWNYRPGHCLYGSSCQEA-

Parental  EEGIFILH-GNRGVYHDDKQPAFRAVYEALRNCSFE-DDNIRSLLKPLELELQKTVHTYCGKIYKIFIKQ
          EEGI.IL...NR.VYHDDKQPAFRAVYEALRNCSF..DDN..SL.KPLELELQ.TVHTY.GKIYKIF.KQ
Retrocopy EEGILILQ<ANRRVYHDDKQPAFRAVYEALRNCSFK<DDNAHSLMKPLELELQQTVHTYRGKIYKIFVKQ

Parental  LAKSVRDRYARSPKEK
          LAKS.RDRYARSPKE.
Retrocopy LAKSIRDRYARSPKER

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	0.88 RPM
SRP007412_cerebellum	0.00 RPM	2.31 RPM
SRP007412_heart	0.00 RPM	2.08 RPM
SRP007412_kidney	0.00 RPM	1.39 RPM
SRP007412_liver	0.00 RPM	1.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1849 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1849 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1849 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151233	5 retrocopies	retro_hsap_2295, retro_hsap_4167, retro_hsap_4177, retro_hsap_4258, retro_hsap_4267,
Gorilla gorilla	ENSGGOG00000027928	3 retrocopies	retro_ggor_1702, retro_ggor_1950, retro_ggor_2798,
Monodelphis domestica	ENSMODG00000008913	1 retrocopy	retro_mdom_512,
Mus musculus	ENSMUSG00000036197	1 retrocopy	retro_mmus_2325,
Nomascus leucogenys	ENSNLEG00000017947	1 retrocopy	retro_nleu_2700,
Pongo abelii	ENSPPYG00000004419	2 retrocopies	retro_pabe_1849 , retro_pabe_1976,
Pan troglodytes	ENSPTRG00000004836	5 retrocopies	retro_ptro_1623, retro_ptro_2832, retro_ptro_2960, retro_ptro_3006, retro_ptro_848,
Rattus norvegicus	ENSRNOG00000005234	1 retrocopy	retro_rnor_2754,