Sequence
atgc intronic sequence ATGC exonic sequencegtaatggacttcaacgacgtgaattgctacgggttttttatttacaggaagacgagtcatttctattcatctttatatatagccatcaatctaatcaatttctgctttccaacactcctaacgaggttctggacttttatggagccagGTTGCCAATGTTGTTCATTCTGCTCCAACGACCAAGGTCTTGTACTTCACAGGAGCAACCAATATTCTGTACACCTTTGGTGGTCACGCTGTTACTGT
Basic information
species | Physcomitrella patens |
transcript | PP1S90_46V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S90_46V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA07G17810.1 (Glycine max), 3'ss of exon 6
gtaatggacttcaacgacgtgaattgctacgggttttttatttacaggaagacgagtcatttctattcatctttatatatagccatcaatctaatcaatttctgctttc-caacactcctaacgaggttctggacttttatggagccagGTTGCCAATGTTGTTCATTCTGCTCCAACGACCAAGGTCTTGTACTTCACAGGAGCAACCAATATTCTGTACACCTTTGGTGGTCACGCTGTTACTGT
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----------------------------------attctaattttatta-------ttgtttttaatgagtattttat-tagtgtttgaaaacatcgttgtatgctaggataatatttttgt----gtgtggaaatattatgg---cagGCAGAAAATGTGACACACACGGGTCCAACGAAGCTAGTGCTGTACTTCACAGGAGCCACCAACATACTGTACACGTTTGGTGGACATGCAGTTACTGT
upper sequence: PP1S90_46V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaatggacttcaacgacgtgaattgctacgggttttttatttacaggaagacgagtcat-ttctattcatctttatatatagccatcaatctaatcaatttctgctttccaacactcctaacgaggttctggacttttatggagccagGTTGCCAATGTTGTTCATTCTGCTCCAACGACCAAGGTCTTGTACTTCACAGGAGCAACCAATATTCTGTACACCTTTGGTGGTCACGCTGTTACTGT
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------------------------------------gtcattataattaacacaaatcttgttttgattattataagatatagacatatagtc--ctggttattgttgtttaatatattta------tttt----tcatataaaaa-agGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
upper sequence: PP1S90_46V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
----gtaatggacttcaacgacgtgaattgctacgggttttttatttacaggaagacgagtcatttctattcatctttatatatagccatcaatctaatcaatttctgctttccaacactcctaacgaggttctggacttttatggagccagGTTGCCAATGTTGTTCATTCTGCTCCAACGACCAAGGTCTTGTACTTCACAGGAGCAACCAATATTCTGTACACCTTTGGTGGTCACGCTGTTACTGT
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gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataatccc-atcccccctttgata----cattgatttattta----------ttaagtaatcccatgctgattt---gcttgtttgaag- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaatttctgctttccaacactcctaacgaggttctggacttttatggagccagGTTGCCAATGTTGTTCATTCTGCTCCAACGACCAAGGTCTTGTACTTCACAGGAGCAACCAATATTCTGTACACCTTTGGTGGTCACGCTGTTACTGT
tcctaac putative branch site (score: 1)
cttttat putative PPT
acttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggacttcaacgacgtgaattgctacgggttttttatttacaggaagacgagtcatttctattcatctttatatatagccatcaatctaatcaatttctgctttccaacactcctaacgaggttctggacttttatggagccagGTTGCCAATGTTGTTCATTCTGCTCCAACGACCAAGGTCTTGTACTTCACAGGAGCAACCAATATTCTGTACACCTTTGGTGGTCACGCTGTTACTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT