Sequence
atgc intronic sequence ATGC exonic sequence...ctgaggttacagttctgcacctcttaatcgttacaaccatccatcaatttgtgtccatttctttcactaatcatgttcttttttggggttgtctttgtagGTTGCACAGACCCATCCACTGGCAGTTGCCAACTGCAATGTTGACATGGAAAGTCTCATTTCTGACCAAAACCGCAGCATTGCTACTCTAGCCATCACTA
Basic information
species | Physcomitrella patens |
transcript | PP1S276_96V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 8
ctgaggttacagttctgc-acctcttaatcgttacaaccatccatcaatttgtgtccatttctttcactaatcatgttc-ttttttggggtt---gtctttgtagGTTGCACAGACCCATCCACTGGCAGTTGCCAACTGCAATGTTGACATGGAAAGTCTCATTTCTGACCAAAACCGCAGCATTGCTACTCTAGCCATCACTA
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--aaatcaataccttcactggtccctaaatattctaatgagatttg---ccgtggtcaaccatgacaaggtttttaatcattaagtgtgacttgaaacttggcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA
upper sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 8
ctgaggttacagttctgc-acctcttaatcgttacaacca--tccatca-atttgtgtccatttctttcactaatcat--gttcttttttggggttgtctttgtagGTTGCACAGACCCATCCACTGGCAGTTGCCAACTGCAATGTTGACATGGAAAGTCTCATTTCTGACCAAAACCGCAGCATTGCTACTCTAGCCATCACTA
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--aaatcaagactttcgctgttccctaaatattctaatgagatttgccatggtcaaacatgtcacggtttttaatcattaagtgtgtcttgaaa----cttgacagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTCGCTATTACTAMapped 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|162254848|gb|FC430825.1|FC430825EST: GCTCATCCAAGCCAGTTTTGCGTTTTGCGGCCGTGCGAACACTCAACAAG GTTGCACAGACCCATCCACTGGCAGTTGCCAACTGCAATGTTGACATGGAA
genomic: GCTCATCCAAGCCAGTTTTGCGTTTTGCGGCCGTGCGAACACTCAACAAGgtgcgtctaa ... gtctttgtagGTTGCACAGACCCATCCACTGGCAGTTGCCAACTGCAATGTTGACATGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttgtgtccatttctttcactaatcatgttcttttttggggttgtctttgtagGTTGCACAGACCCATCCACTGGCAGTTGCCAACTGCAATGTTGACATGGAAAGTCTCATTTCTGACCAAAACCGCAGCATTGCTACTCTAGCCATCACTA
cactaat putative branch site (score: 2)
ttgtcttt putative PPT
ttctttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgaggttacagttctgcacctcttaatcgttacaaccatccatcaatttgtgtccatttctttcactaatcatgttcttttttggggttgtctttgtagGTTGCACAGACCCATCCACTGGCAGTTGCCAACTGCAATGTTGACATGGAAAGTCTCATTTCTGACCAAAACCGCAGCATTGCTACTCTAGCCATCACTA
- - - - - - ttctgca