Sequence
atgc intronic sequence ATGC exonic sequencegtatatgcctaatcccagttgactgtgtgaacctcgttctgatgcatgatttcaacctactttttcattttgtatgaatctatggaatactcttatacagattaacatcagcactggccttgccaaatcaataaatgtatctacagtgcaatgatttcactgactcgaagttatgaattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCAAATCAGTTGCAGCTGGCATGAACGCAATGGACCTACGTAGAGGTATTAG
Basic information
species | Physcomitrella patens |
transcript | PP1S378_9V6.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
gtatatgcctaatcccagttgactgtgtgaacctcgttctgatgcatgatttcaacctactttttcattttgtatgaatctatggaatactcttatacagattaacatcagcactggccttgccaaatcaat-aaatgtatctacagtgcaatgatttcactgactcgaagttatgaattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCAAATCAGTTGCAGCTGGCATGAACGCAATGGACCTACGTAGAGGTATTAG
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-----------------------------------------------------------------------------------tgaagactgtaa-accaactatcagct-tgctggtattatctaataatttaggtgctgttaccatgaaagaatattgagggaac-atttcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 4
gtatatgcctaatcccagttgactgtgtgaacctcgttctgatgcatgatttcaacctactttttcattttgtatgaatctatggaatactcttatacagattaacatcagcactggc-cttgccaaatcaataaatgtatctacagtgcaatgatttcactgactcgaagttatgaatt---ttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCAAATCAGTTGCAGCTGGCATGAACGCAATGGACCTACGTAGAGGTATTAG
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----------------------------------------------------------------------------------------gactataaactgactatcagct-tgctggtatttatccaataattaggtgttgttaccgtgacagaatattgagggagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatatgcctaatcccagttgactgtgtgaacctcgttctgatgcatgatttcaacctactttttcattttgtatgaatctatggaatactcttatacagattaacatcagcactggccttgccaaatcaataaatgtatctacagtgcaatgat-ttcactgactcgaagtta-tgaattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCAAATCAGTTGCAGCTGGCATGAACGCAATGGACCTACGTAGAGGTATTAG
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----------------------------------------------------------------------------------------------gtaagatatttcattttgattgattatgc--ggttcatagttgtagaaactttgcaaaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 4
gtatatgcctaatcccagttgactgtgtgaacctcgttctgatgcatgatttcaacctactttttcattttgtatgaatctatggaatactcttatacagattaacatcagcactggccttgccaaatcaataaatgtatctacagtgcaatgatttcactgactcgaagttatgaattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCAAATCAGTTGCAGCTGGCATGAACGCAATGGACCTACGTAGAGGTATTAG
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----------------------------------------------------------------------agaatggttttatgaca-------atgcatact--tgtctacgttgtctctgt-ggtttattt--tgtttctgttacacatagatctgat---cccttatttttgatgatttcagGTACCACCTGTGCCACAGTCCTTACCCGAGCAATATTTACTGAAGGGTGCAAGTCGGTTGCTGCTGGAATGAATGCAATGGACCTAAGAAGGGGTATCTCMapped 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|162181241|gb|FC357647.1|FC357647EST: ATCACTCGTGAAGTCAGTCGCTAGTTCTACAAATGACGTTGCTGGAGATG GAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCA
genomic: ATCACTCGTGAAGTCAGTCGCTAGTTCTACAAATGACGTTGCTGGAGATGgtatatgcct ... aattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCA
EST:
gi|162155518|gb|FC330988.1|FC330988EST: ATCACTCGTGAAGTCAGTCGCTAGTTCTACAAATGACGTTGCTGGAGATG GAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCA
genomic: ATCACTCGTGAAGTCAGTCGCTAGTTCTACAAATGACGTTGCTGGAGATGgtatatgcct ... aattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCA
EST:
gi|162199529|gb|FC373181.1|FC373181EST: ATCACTCGTGAAGTCAGTCGCTAGTTCTACAAATGACGTTGCTGGAGATG GAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCA
genomic: ATCACTCGTGAAGTCAGTCGCTAGTTCTACAAATGACGTTGCTGGAGATGgtatatgcct ... aattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaatgtatctacagtgcaatgatttcactgactcgaagttatgaattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCAAATCAGTTGCAGCTGGCATGAACGCAATGGACCTACGTAGAGGTATTAG
cactgac putative branch site (score: 2)
aagttatgaatttt 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
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gtatatgcctaatcccagttgactgtgtgaacctcgttctgatgcatgatttcaacctactttttcattttgtatgaatctatggaatactcttatacagattaacatcagcactggccttgccaaatcaataaatgtatctacagtgcaatgatttcactgactcgaagttatgaattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCAAATCAGTTGCAGCTGGCATGAACGCAATGGACCTACGTAGAGGTATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG