RetrogeneDB ID: retro_pabe_1225

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:30611268..30612404(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FSCN1
• Ensembl ID: ENSPPYG00000017337
• Aliases: None
• Description: fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus) [Source:HGNC Symbol;Acc:11148]

Sequence

>retro_pabe_1225
CTCCCGTCCACCGCCACCATGACCGCCAACTGCACAGCCGAGGCAGTGCAGATCCAGTTCGGCCTCATCAACTGCGGCAA
CAAGTACCTGACGGCCGAGGCATTCGGGTTCAAGGTTAACGCGTCGGCCAGCAGCCTGAAGAAGAAGCAGATCTGGATGC
CGGAGCAGCACCCTGACGAGGCGGGCAGCGCGGCCGTGTGCCTGCGCAGCCACCTGGGCCGCTACCTGGCGGCGGACAAG
GACGGCAACGTGACCTGCGAGCGCGAGGTGCCCGGTCCCGACTGCCGCTTCCTCATCGTGGTGCACGACGACGGCCGCTG
GTCGCTGCAGTCCGAGGAGCACCGGCGCTACTTCGGAGGCACCGAGGACCGCCTGTCTGCTTCGCGCAGACGGTGTCCCC
CGCCGAGAAGCGGAGCGTGCACATCGCCATGCACCCTCAGGTCAACATCTACAGCGTCACCCGTAGGCGCTAGGCGCACC
TGAGCGCACGGCCGGCCGACGAGATCGCCGTGGACCGCGACGTGCCCTGGGGCAACGACTCGCTCATCATCCTCGCCTTC
CAGGACCAGCGCTACAGAGTGCAGACCGCCGACCACCGCTTCCTGCGCCATGACGGGCGCCTGGTGGCGAGCCCCGAGCC
GGCCACTGGCTACACGCTGGAGTTCCGCTTCGGCAAGGTGGCCTTCCGCGACTGCGAGGGTCCTTACCTGGCGCCGTCGG
GGCCCAGCAACACGCTCAAGGCTGGCAAGGCCACCAAGGTGGGCAAGGACGAGCTCTTTGCCCTGGAGCAGAGCTGCGCC
CAGGTCGTGCTGCAGGCGGCCAACGAGAGGAATGTGTCCACGCGCCAGGGTAAGGACCTGTCTGCCAATCAGGAGGAGGA
GACCGACCAGGAGACCTTCCAGCTGGAGATCTACCGCGACACCAAAAAGTGTGCCTTCCGTACCCACACGGGCAAGTACT
GGACGCTGACGGCCACTGGGGGCGTGCAGTCCACCGCCTCCACCCAGAATGCCAGCTGCTACTTCGACATTGAGCGGCGT
GACCGGCGCATCACACTGCGGGCGTCCAATGGCAAGTTTGTGACATCTAAGAAGAATGGGCAGCTGGCCGCCTCGGTGGA
GACAGCAGGGGACTCA

Alignment

ORF - retro_pabe_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.95 %
• Parental protein coverage: 85.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSSTATMTANGTAEAVQIQFGLINCGNKYLTAEAFGFKVNASASSLKKKQIWTLEQPPDEAGSAAVCLRS
          L.STATMTAN.TAEAVQIQFGLINCGNKYLTAEAFGFKVNASASSLKKKQIW..EQ.PDEAGSAAVCLRS
Retrocopy LPSTATMTANCTAEAVQIQFGLINCGNKYLTAEAFGFKVNASASSLKKKQIWMPEQHPDEAGSAAVCLRS

Parental  HLGRYLAADKDGNVTCEREVPGPDCRFLIVAHDDGRWSLQSEAHRRYFGGTEDRLS-CFAQTVSPAEKWS
          HLGRYLAADKDGNVTCEREVPGPDCRFLIV.HDDGRWSLQSE.HRRYFGGTEDRLS.CFAQTVSPAEK.S
Retrocopy HLGRYLAADKDGNVTCEREVPGPDCRFLIVVHDDGRWSLQSEEHRRYFGGTEDRLS<CFAQTVSPAEKRS

Parental  VHIAMHPQVNIYSVTRKRYAHLSARPADEIAVDRDVPWGVDSLITLAFQDQRYSVQTADHRFLRHDGRLV
          VHIAMHPQVNIYSVTR.R.AHLSARPADEIAVDRDVPWG.DSLI.LAFQDQRY.VQTADHRFLRHDGRLV
Retrocopy VHIAMHPQVNIYSVTRRR*AHLSARPADEIAVDRDVPWGNDSLIILAFQDQRYRVQTADHRFLRHDGRLV

Parental  ARPEPATGYTLEFRSGKVAFRDCEGRYLAPSGPSGTLKAGKATKVGKDELFALEQSCAQVVLQAANERNV
          A.PEPATGYTLEFR.GKVAFRDCEG.YLAPSGPS.TLKAGKATKVGKDELFALEQSCAQVVLQAANERNV
Retrocopy ASPEPATGYTLEFRFGKVAFRDCEGPYLAPSGPSNTLKAGKATKVGKDELFALEQSCAQVVLQAANERNV

Parental  STRQGMDLSANQDEETDQETFQLEIDRDTKKCAFRTHTGKYWTLTATGGVQSTASTKNASCYFDIEWRDR
          STRQG.DLSANQ.EETDQETFQLEI.RDTKKCAFRTHTGKYWTLTATGGVQSTAST.NASCYFDIE.RDR
Retrocopy STRQGKDLSANQEEETDQETFQLEIYRDTKKCAFRTHTGKYWTLTATGGVQSTASTQNASCYFDIERRDR

Parental  RITLRASNGKFVTSKKNGQLAASVETAGDS
          RITLRASNGKFVTSKKNGQLAASVETAGDS
Retrocopy RITLRASNGKFVTSKKNGQLAASVETAGDS

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	36.22 RPM
SRP007412_cerebellum	0.00 RPM	5.84 RPM
SRP007412_heart	0.12 RPM	0.90 RPM
SRP007412_kidney	0.00 RPM	4.94 RPM
SRP007412_liver	0.00 RPM	7.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1225 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1225 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000075618	1 retrocopy	retro_hsap_1476,
Monodelphis domestica	ENSMODG00000001028	1 retrocopy	retro_mdom_423,
Ornithorhynchus anatinus	ENSOANG00000030243	1 retrocopy	retro_oana_11,
Pongo abelii	ENSPPYG00000017337	3 retrocopies	retro_pabe_1225 , retro_pabe_3201, retro_pabe_3544,