RetrogeneDB ID: retro_ptro_1669

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:204373577..204374428(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSPTRG00000002303
• Aliases: None
• Description: Pan troglodytes selenophosphate synthetase 1 (SEPHS1), mRNA. [Source:RefSeq mRNA;Acc:NM_001145817]

Sequence

>retro_ptro_1669
AATGTCCTCAGTGACCTCTACGCAACGAGGGTCATGGAATGCAACAATATGCTGATGCTCCTTGGAGTCAGTAATAAAAT
GACTGACAGGGAAAGGGATGAAGTGATGCCTCTGATTATCCAAGGTTTTAAAGACGCAGCTGAAGAAGCAGGAACGTCTG
TAACAGGCGGCCAAACAGTTCTAAACCCCTGGATTGTCCTGGGAGGAGTCGCTACCACTGTCTGCCAGCCCAATGAATTT
ATCATGCAGACAATGCAGTGCCAGGAGACATGCTGGTGTAGACAAAACCCCTGGGGACACAGGTGGCAGTGGCTGTGCAC
CAGTGGCTGGATATTCCTGAGAAATGGAATAAGATTAAACTAGTGGTCACCCAAGAAGATGTAGAGCTGGCCTACCAGGA
GGCGATGATGAACATGGCAAGGCTCAACGGGACAGCTGCCGGACTCATGCACACGTTCAATGCCCACGCGGCCACTGACA
TCAAGGGCTTTGGGATTTGGAGCCATGTGCAGAACCTGGCCAAGCAGCAGAGGAACGAGGTGTCATTTGTAATTCACAGC
CTCCCGGCGCTGGCCAAGATGGCTGCAGCGAGCAAGGCGTGCGGAAACATGTTCGGCCTCATGCACAGGACCTGCCCAGA
GACCTCAGGCGGCCTTCTGATCTGTTTACCACATCAGCAAGCAGCTCGGTTCTGTGCAGAGATAAAGTCCCCCAAATATG
GTGAAGGCCACCAAGCATGGATTATTGGGATTGTAGAGAAGGGCAACTGCACAGCCAGAATCATAGACAAACCCTGGATC
ATCGAGGTCGCACCACAAGTGGCCACCCAAAATATGAATCCCACACCCGGG

Alignment

ORF - retro_ptro_1669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.93 %
• Parental protein coverage: 72.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGV
          NVLSDLYA..V.EC.NMLMLLGVSNKMTDRERD.VMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGV
Retrocopy NVLSDLYATRVMECNNMLMLLGVSNKMTDRERDEVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGV

Parental  ATTVCQPNEFIMP-DNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNM
          ATTVCQPNEFIM..DNAVPGD.LV.TKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNM
Retrocopy ATTVCQPNEFIMQ<DNAVPGDMLV*TKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNM

Parental  ARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMH
          ARLN.TAAGLMHTFNAHAATDI.GFGI..H.QNLAKQQRNEVSFVIH.LP.LAKMAA.SKACGNMFGLMH
Retrocopy ARLNGTAAGLMHTFNAHAATDIKGFGIWSHVQNLAKQQRNEVSFVIHSLPALAKMAAASKACGNMFGLMH

Parental  GTCPETSGGLLICLPREQAARFCAEIKSPKYGEGHQAWIIGIVEKGNRTARIIDKPRIIEVAPQVATQNV
          .TCPETSGGLLICLP..QAARFCAEIKSPKYGEGHQAWIIGIVEKGN.TARIIDKP.IIEVAPQVATQN.
Retrocopy RTCPETSGGLLICLPHQQAARFCAEIKSPKYGEGHQAWIIGIVEKGNCTARIIDKPWIIEVAPQVATQNM

Parental  NPTPG
          NPTPG
Retrocopy NPTPG

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	0.16 RPM	19.22 RPM
SRP007412_cerebellum	0.00 RPM	33.91 RPM
SRP007412_heart	0.00 RPM	14.25 RPM
SRP007412_kidney	0.00 RPM	48.41 RPM
SRP007412_liver	0.00 RPM	31.13 RPM
SRP007412_testis	0.11 RPM	17.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1669 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1669 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2196
Pongo abelii	retro_pabe_2074
Macaca mulatta	retro_mmul_922

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Dipodomys ordii	ENSDORG00000014119	1 retrocopy	retro_dord_792,
Equus caballus	ENSECAG00000014281	1 retrocopy	retro_ecab_77,
Homo sapiens	ENSG00000086475	3 retrocopies	retro_hsap_2196, retro_hsap_3860, retro_hsap_4705,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Mus musculus	ENSMUSG00000026662	1 retrocopy	retro_mmus_248,
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,
Otolemur garnettii	ENSOGAG00000007807	1 retrocopy	retro_ogar_3026,
Pan troglodytes	ENSPTRG00000002303	3 retrocopies	retro_ptro_1135, retro_ptro_1669 , retro_ptro_3126,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,