Sequence
atgc intronic sequence ATGC exonic sequence...gtgtttaattcagttatgttttagggtgcttgttgaggatcttgaagttggcttgtcgaagtaaacttcttctgaagttaatcttggatgatggtgccagACAGTCGCTCTTTTCAAGTCGTATTTCGGAGGGGCGTTCGATGAAGATGCGATCAGAAACAACTTTGTGCTTATCTACGAGCTTCTTGATG
Basic information
species | Physcomitrella patens |
transcript | PP1S197_28V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 2
---gtgtttaattc-agttatgttttagggtgcttgttgaggatcttgaagttggcttgtcgaagtaaacttcttctgaagttaatcttggatgatggtgccagACAGTCGCTCTTTTCAAGTCGTATTTCGGAGGGGCGTTCGATGAAGATGCGATCAGAAACAACTTTGTGCTTATCTACGAGCTTCTTGATG
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tcagttataaattctagacatatatccttctgatacctgcatatcatcct-ctagtgttttgaacggttttttatgtatgattttttttgta-aat--taccagGCAGTGGCTCTTTTCAAGTCATACTTTGGTGGTGCTTTTGATGAAGATGCTATCAGAAATAACTTTGTTTTAATCTATGAGCTTCTTGATG
upper sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 2
gtgtttaattcagttatgttttagggtgcttgttgaggatcttgaagttggcttgtcgaagtaaacttcttctgaagttaatcttggatgatggtgccagACAGTCGCTCTTTTCAAGTCGTATTTCGGAGGGGCGTTCGATGAAGATGCGATCAGAAACAACTTTGTGCTTATCTACGAGCTTCTTGATG
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-----------------gtct----acgctt-tcagagattttgt--ttctcttgttct--taaactttgct-----cctttctcgttggtttttcacagGCTGTGGCTCTTTTCAAGAGTTATTTCGGTGGTGCTTTTGATGAGGACGCTATCAGAAATAACTTTGTGCTCATCTACGAGCTTCTCGACG
upper sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 2
gtgtttaattcagttatgttttagggtgcttgttgaggatcttgaagttggcttgtcgaagtaaacttcttctgaagttaatcttggatgatggtgccagACAGTCGCTCTTTTCAAGTCGTATTTCGGAGGGGCGTTCGATGAAGATGCGATCAGAAACAACTTTGTGCTTATCTACGAGCTTCTTGATG
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-----------------gtct----acactt-tcagagattttgt--ttctcttgttct--taaactttgct-----cctttctcgttggtttttcacagGCTGTGGCTCTTTTCAAGAGTTATTTCGGTGGTGCTTTTGATGAGGACGCTATCAGAAATAACTTTGTGCTCATCTACGAGCTTCTCGACGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|208358886|gb|DC935216.1|DC935216EST: TTGTTAGCAGCAATGCCAATGCCGCATGCGCTTTCAAATTCATGGTTGAG ACAGTCGCTCTTTTCAAGTCGTATTTCGGAAGGGCCGTTCGATGAANATGC
genomic: TTGTTAGCAGCAATGCCAATGCCGCATGCGCTTTCAAATTCATGGTTGAGgtatattctg ... atggtgccagACAGTCGCTCTTTTCAAGTCGTATTTCGGAGGGGC-GTTCGATGAAGATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttggcttgtcgaagtaaacttcttctgaagttaatcttggatgatggtgccagACAGTCGCTCTTTTCAAGTCGTATTTCGGAGGGGCGTTCGATGAAGATGCGATCAGAAACAACTTTGTGCTTATCTACGAGCTTCTTGATG
agttaat putative branch site (score: 4)
aagttaat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttaattcagttatgttttagggtgcttgttgaggatcttgaagttggcttgtcgaagtaaacttcttctgaagttaatcttggatgatggtgccagACAGTCGCTCTTTTCAAGTCGTATTTCGGAGGGGCGTTCGATGAAGATGCGATCAGAAACAACTTTGTGCTTATCTACGAGCTTCTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT