RetrogeneDB ID: retro_pabe_821

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:10397583..10398204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPAB
• Ensembl ID: ENSPPYG00000016107
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A/B [Source:HGNC Symbol;Acc:5034]

Sequence

>retro_pabe_821
ATGCTTGTTGGTGGCCTGAGCTGGGATACCAGCAAAAAGGATTTAAAGGACCGTTTTACTAAATTTGGAGAAGTCATTGA
CTGTACAATAAAAATGGATCCCAACACTGGATGGGCAAGAGGGTTTGGGTTTATCCTGTTCAAAGATGCAACCAATGTGG
AGAAGGTCCTAGACCAGAAGGAGTACAGGCTGGATGTCCGTGTCATTGACCCTAAAAAGGCCATGGCTATGAAGAAGGAC
CGGGTGAAGAAAATCTTCGTCGAGGGTCTGAATCCTGAAGCCACTGAGGAAAAGATCAGGGAGTACTTTGGCGAGTTTGG
GGAGATCGAGGCCATTGAAATTCCAGTGGATCCAAAGTTGAACAAAAGACAAGGTTTTGTGTTTATCTCCTTTAAAAAAG
AAGAACCTATGAAGAAAGTTCTGGAGAAAAAGTTCCATACTATCAGTGGAAGTAAGCGTGAGATCAAGGTGGCCCAGCCC
AAAGTTTATTGGCAGCAACGGTATGGTTCTGGGGACCGTGGAAACCACAACCGAGGGAACCGAGGCAGCGGAGGTGGTGG
TGGAGGTGGAGGTCAGGGCACAAACTACAGCAAGAGCCAGCGACATGGTGGCCATCAGAAT

Alignment

ORF - retro_pabe_821 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 78.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVID
          M.VGGLSWDTSKKDLKD.FTKFGEV.DCTIKMDPNTG..RGFGFILFKDA..VEKVLDQKE.RLD.RVID
Retrocopy MLVGGLSWDTSKKDLKDRFTKFGEVIDCTIKMDPNTGWARGFGFILFKDATNVEKVLDQKEYRLDVRVID

Parental  PKKAMAMKKDPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKLNKRRGFVFITFKEEEPVKKV
          PKKAMAMKKD.VKKIFV.GLNPEATEEKIREYFGEFGEIEAIE.P.DPKLNKR.GFVFI.FK.EEP.KKV
Retrocopy PKKAMAMKKDRVKKIFVEGLNPEATEEKIREYFGEFGEIEAIEIPVDPKLNKRQGFVFISFKKEEPMKKV

Parental  LEKKFHTISGSKXEIKVAQPKEVYQQQQYGSGGRGNRNRGNRGSGGGGGGGGQSQSW--NQGYGNYWN
          LEKKFHTISGSK.EIKVAQPK.VY.QQ.YGSG.RGN.NRGNRGS........Q.......Q..G...N
Retrocopy LEKKFHTISGSKREIKVAQPK-VYWQQRYGSGDRGNHNRGNRGSXXXXXXXXQGTNYSKSQRHGGHQN

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	0.66 RPM	12.88 RPM
SRP007412_cerebellum	0.85 RPM	8.03 RPM
SRP007412_heart	1.41 RPM	12.46 RPM
SRP007412_kidney	1.52 RPM	26.52 RPM
SRP007412_liver	1.41 RPM	20.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_821 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_821 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_821 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_962
Pan troglodytes	retro_ptro_666

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000241	2 retrocopies	retro_cfam_408, retro_cfam_412,
Homo sapiens	ENSG00000197451	1 retrocopy	retro_hsap_962,
Loxodonta africana	ENSLAFG00000001189	1 retrocopy	retro_lafr_405,
Macropus eugenii	ENSMEUG00000007909	2 retrocopies	retro_meug_169, retro_meug_246,
Myotis lucifugus	ENSMLUG00000003380	2 retrocopies	retro_mluc_2024, retro_mluc_2138,
Nomascus leucogenys	ENSNLEG00000015775	1 retrocopy	retro_nleu_1611,
Oryctolagus cuniculus	ENSOCUG00000026424	3 retrocopies	retro_ocun_1800, retro_ocun_1811, retro_ocun_950,
Otolemur garnettii	ENSOGAG00000030251	2 retrocopies	retro_ogar_3509, retro_ogar_385,
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,
Pan troglodytes	ENSPTRG00000017601	1 retrocopy	retro_ptro_666,