RetrogeneDB ID: retro_pabe_2074

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:90712826..90713858(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSPPYG00000002099
• Aliases: None
• Description: Selenide, water dikinase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5RF87]

Sequence

>retro_pabe_2074
ACGCGGGAGTCCTTTTAACCCAGAAAGTTACGAATTGGACAGGAGCTTCTGGCTAACCAGATTCACTGAACTGAATGGCA
CAGGCTGCAAAGTGCCCCAAGATGTCCTGCAAAAATAGCTGGAATCTTTACAGGAGAACCACTTCCAAGAAGATGAGCAG
TTTTTGGGAGTCGTTAGGCCAAGCCTTGGCATTGGAATGGATACTTGTGTCATTCCTTTGAGGCATGGTGGGCTTTCCTT
GGTTCAAACCATAGATTACATTTACCCGATCGTAGATGACCCTTACATGATGGGCAGGATAGCATGTGTCAATGTCCTCA
GTGACCTCTACGCAACGGGGGTCATGGAATGTGACAATATGCTGGTGCTCCTTGGAGTCAGTAATAAAATGACTGACAGG
GAAAGGGATAAAGTGATGCCTCTGATTATCCAAGGTTTTAAAGACGCAGCTGAAGAAGCAGGAACATATGTAACAGGCGG
CCAAACCGTTCTAAACCCCTGGATTGTCCTGGGAGGAGTTGCTACCACTGTCTGTCAGCCCAATTAATTTATCCTGCCAG
ACAATGCAGTGCCAGGAAACGTGCTGGTGTAGACAAAACCCCTGGGGACACAGGTGGCAATGGCTGTGCACCAGTGGCTG
GATATTCCTGAGAAATGGAATAAGATTAAACTAGTGGTCACCCAAGAAGATGTAGAGCTGCTCTACCAGGAAGCGATGAT
GAACATGGCGAGGCTCAACAGGACGGCTGCCGGACTTATGCACACGTTCAATGCCCACGCAGCCACTGACATCATGGGCT
TTGGGATTTTGGGCCATGTGCAGAACCTGGCCAAGCAGCAGAGGAACGAGGTGTCATTTGTAATTCACAACCTCCTGGTG
CTGGCCAAGATGGCTGCAGCGAGCAAGGCATGCGGAAACATGTTCGGCCTCATGCACGGGACCTGCCCAGAGACCTCAGG
TGGCCTTCTGATCTGTTTACCACATCAGCAAGCAGCTCGGTTCTGTGCAGAGATAAACTCCCCCAAATATGG

Alignment

ORF - retro_pabe_2074 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.62 %
• Parental protein coverage: 99.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TRESF-NPESYELDKSFRLTRFTELKGTGCKVPQDVLQKLLESLQENHFQEDEQFLGAVMPRLGIGMDTC
          TRESF.NPESYELD.SF.LTRFTEL.GTGCKVPQDVLQK.LESLQENHFQEDEQFLG.V.P.LGIGMDTC
Retrocopy TRESF>NPESYELDRSFWLTRFTELNGTGCKVPQDVLQK*LESLQENHFQEDEQFLGVVRPSLGIGMDTC

Parental  VIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVM
          VIPLRHGGLSLVQT.DYIYPIVDDPYMMGRIAC.NVLSDLYA.GV.ECDNML.LLGVSNKMTDRERDKVM
Retrocopy VIPLRHGGLSLVQTIDYIYPIVDDPYMMGRIACVNVLSDLYATGVMECDNMLVLLGVSNKMTDRERDKVM

Parental  PLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAV
          PLIIQGFKDAAEEAGT.VTGGQTVLNPWIVLGGVATTVCQPN.FI.PDNAVPG.VLV.TKPLGTQVA.AV
Retrocopy PLIIQGFKDAAEEAGTYVTGGQTVLNPWIVLGGVATTVCQPN*FILPDNAVPGNVLV*TKPLGTQVAMAV

Parental  HQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQ
          HQWLDIPEKWNKIKLVVTQEDVEL.YQEAMMNMARLNRTAAGLMHTFNAHAATDI.GFGILGH.QNLAKQ
Retrocopy HQWLDIPEKWNKIKLVVTQEDVELLYQEAMMNMARLNRTAAGLMHTFNAHAATDIMGFGILGHVQNLAKQ

Parental  QRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCG-RDKVPQIW
          QRNEVSFVIHNL.VLAKMAA.SKACGNMFGLMHGTCPETSGGLLICLP..QAARFC..RDK.PQIW
Retrocopy QRNEVSFVIHNLLVLAKMAAASKACGNMFGLMHGTCPETSGGLLICLPHQQAARFCA<RDKLPQIW

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	0.28 RPM	19.85 RPM
SRP007412_cerebellum	0.12 RPM	29.79 RPM
SRP007412_heart	0.06 RPM	8.34 RPM
SRP007412_kidney	0.20 RPM	32.65 RPM
SRP007412_liver	0.12 RPM	17.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2074 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2074 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2074 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2196
Pan troglodytes	retro_ptro_1669
Macaca mulatta	retro_mmul_922

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Felis catus	ENSFCAG00000003921	1 retrocopy	retro_fcat_96,
Macropus eugenii	ENSMEUG00000012188	1 retrocopy	retro_meug_245,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Mustela putorius furo	ENSMPUG00000000948	1 retrocopy	retro_mputfur_20,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Pongo abelii	ENSPPYG00000002099	6 retrocopies	retro_pabe_1324, retro_pabe_1378, retro_pabe_2074 , retro_pabe_2620, retro_pabe_3047, retro_pabe_3652,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,