Sequence
atgc intronic sequence ATGC exonic sequenceCCTTTCTACTGTGAGGGCACTTGACGCTTTGGACTTGGATGTGCAACAGGCCGTCATCAGCTGCTTCAATGGCTTTGCTCTAGACCTCTTCCGCGCTGAGgtaagcagagccagaccaacccccaaaccctaaacctgaaaaatcacgctgtcacttgcaaaattacaagagctcgcgtgtgtactaagtgtcgtaaaaatggccagcctcttttggttcaggccctgtactgatgcactttgggcgaggtttaatggaattgccag
Basic information
species | Physcomitrella patens |
transcript | PP1S212_62V6.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S212_62V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G173534_T02 (Zea mays), 5'ss of exon 3
CCTTTCTACTGTGAGGGCACTTGACGCTTTGGACTTGGATGTGCAACAGGCCGTCATCAGCTGCTTCAATGGCTTTGCTCTAGACCTCTTCCGCGCTGAGgtaagcaga-gccagaccaacccccaaaccctaaacctgaaaaatc--acgctgtcactt--gcaaaattacaagagctcgcgtgtgtactaagtgtcgtaaaaatggccagcctcttttggttcaggccctgtactgatgcactttgggcgaggtttaatggaattgccag
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GCTGTCGACAATGACGGCCCTCGACAGCCTAGGCCTCGACATCGAGCAGGCGGTCATCAGCTGCTTCAATGGCTTTGCGATGGACGTGTTCCGAGCTGAGgtctgtggtcaccacgccaatacc-atttcct----ctgaaaactctgatggattcaattcaaccaaattaccaaacccaccgttgctcacccctgcc-tcttcatgtct---ctctgtcgcctccc-cccag---------------------------------------
upper sequence: PP1S212_62V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G173534_T01 (Zea mays), 5'ss of exon 3
CCTTTCTACTGTGAGGGCACTTGACGCTTTGGACTTGGATGTGCAACAGGCCGTCATCAGCTGCTTCAATGGCTTTGCTCTAGACCTCTTCCGCGCTGAGgtaagcaga-gccagaccaacccccaaaccctaaacctgaaaaatc--acgctgtcactt--gcaaaattacaagagctcgcgtgtgtactaagtgtcgtaaaaatggccagcctcttttggttcaggccctgtactgatgcactttgggcgaggtttaatggaattgccag
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GCTGTCGACAATGACGGCCCTCGACAGCCTAGGCCTCGACATCGAGCAGGCGGTCATCAGCTGCTTCAATGGCTTTGCGATGGACGTGTTCCGAGCTGAGgtctgtggtcaccacgccaatacc-atttcct----ctgaaaactctgatggattcaattcaaccaaattaccaaacccaccgttgctcacccctgcc-tcttcatgtct---ctctgtcgcctccc-cccagcag------------------------------------
upper sequence: PP1S212_62V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv01s0244g00130.t01 (Vitis vinifera), 5'ss of exon 3
CCTTTCTACTGTGAGGGCACTTGACGCTTTGGACTTGGATGTGCAACAGGCCGTCATCAGCTGCTTCAATGGCTTTGCTCTAGACCTCTTCCGCGCTGAGgtaagcagagccagaccaacccccaaaccctaaacctgaaaaatcacgctgtcacttgcaaaattacaagagctcgcgtgtgtactaagtgtcgtaaaaatggccagcctcttttggttcaggccctgtactgatgcactttgggcgaggtttaatggaattgccag
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GCTCTCTGCCATGAGGGCTTTGGATGGCCTTGGGCTAGACGTTCAACAGGCGGTCATCAGCTGTTTCAATGGGTTTGCTCTGGATATCTTCCAAGCTGAGgttagc----------ttccttcaaaatcatattactgtataatcatcaggccctgaacaatacttaaaaa-----cattttgacccttttttcaaaatttaaatcaattctccc----------------------------------------------------Mapped 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|18353094|gb|BJ185149.1|BJ185149EST: CCGTCATCAGCTGCTTCAATGGCTTTGCTCTAGACCTCTTCCGCGCTGAG GCAAAAGATGT
genomic: CCGTCATCAGCTGCTTCAATGGCTTTGCTCTAGACCTCTTCCGCGCTGAGgtaagcagag ... gaattgccagGCAAAAGATGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCTTTCTACTGTGAGGGCACTTGACGCTTTGGACTTGGATGTGCAACAGGCCGTCATCAGCTGCTTCAATGGCTTTGCTCTAGACCTCTTCCGCGCTGAGgtaagcagagccagaccaacccccaaaccctaaacctgaaaaatcacgctgtcacttgcaaaattacaagagctcgcgtgtgtactaagtgtcgtaaaaatggccagcctcttttggttcaggccctgtactgatgcactttgggcgaggtttaatggaattgccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT