Sequence
atgc intronic sequence ATGC exonic sequencegtgcgctatttgttttaaaataataattcaaaacagccgactttagactgattctgaagaaattttcttgttttcatgtagagtgatttggaggtcaactttccaccttgacctatgtctatagctacttgttgtaaagaggtcttgaatattataatttcatcacaatttctgttattgcagGATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S2_272V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S2_272V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G04230.1 (Glycine max), 3'ss of exon 12
gtgcgctatttgttttaaaataataattcaaaacagccgactttagactgattctgaagaaattttcttgttttcatgtagagtgatttggaggtcaactttccaccttgacctatgtctatagctacttgttgtaaagaggtcttgaatattataatttcatcacaatttctgttattgcagGATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAG
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------------------------------------------------------------------------gtgatgtataa--atttagcaataagtttccaatc----catatggacaaaaatataaaaggaaagaaagccat-----ttgcattttcat-----tttgtat-attgcagGATGGAAAAGTTTTACCAGATGGTCCTGTTGTTATTTCCCCTGATGGACTTTTTCCCTCTCTATATCGAGAAG
upper sequence: PP1S2_272V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G04060.1 (Glycine max), 3'ss of exon 11
gtgcgctatttgttttaaaataataattcaaaacagccgactttagactgattctgaagaaattttcttgttttcatgtagagtgatttggaggtcaactttccaccttgacctatgtctatagctacttgttgtaaagaggtcttgaatattataatttcatcacaatttctgttattgcagGATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAG
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------------------------------------------------------------------------gtgatgtgtaa--atttagcaatcagtttctaatc----catatggacaaaaatataaaaggaaataaagctat-----ttacattttcatttttattttgtatattgcagGATGGAAAAGTTTTACCAGATGGTCCTGTTGTTATTTCCCCTGATGGACTTTTTCCCTCTCTATATCGAGAAG
upper sequence: PP1S2_272V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA19G35930.1 (Glycine max), 3'ss of exon 8
gtgcgctatttgttttaaaataataattcaaaacagccgactttagactgattctgaagaaattttcttgttttcatgtagagtgatttggaggtcaactttccaccttgacctatgtctatagctacttgttgtaaagaggtcttgaatattataatttcatcacaatttctgttattgcagGATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAG
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--------------------------------------------------------------ttttttcaatttctttt--------ttttatgtc---cttgcatcttgacaact-----cagtta-tcattgtaaaaatacc----actttaggagatactaaaagttcatatatttgcagGATGGCAAGACCTTACCGAATGGACCTGTTGTTATTTCACCTGATGGATTATTTCCCTCTCTTTACCGAGAAG
upper sequence: PP1S2_272V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA17G36130.1 (Glycine max), 3'ss of exon 7
gtgcgctatttgttttaaaataataattcaaaacagccgactttagactgattctgaagaaattttcttgttttcatgtagagtgatttggaggtcaactttccaccttgacctatgtctatagctacttgttgtaaagaggtcttgaatattataatttcatcacaatttctgttat--tgcagGATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAG
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---------------------------------------------------------------------------gtgataaataagtttcaaatcaatattaa---ttg--ttatggactaaacaagacgaaaaaaaaaagaaagcagt-ttacatcctc-ttattccttttgttatgatgcagGATGGGAAACTTTTACCAGATGGCCCTGTTGTTATATCCCCTGATGGACTCTTTCCTTCTCTATATCGAGAAG
upper sequence: PP1S2_272V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 8
gtgcgctatttgttttaaaataataattcaaaacagccgactttagactgattctgaagaaattttcttgtt--ttcatgtagagtgatttggaggtcaactttccaccttgacctatgtctatagctacttgttgtaaagaggtcttgaatattataatttcatcacaatttctgttattgcagGATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAG
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--------------------------------------------------gtgagggagaattgtttttacttcttgatttgaagtga----gaaatcaaaatttaggaaccctgaatgttt-tatttattt--tattatttattcctttcttttaaaga---atatcatttttcatattttcagGATGGAAAGGCTTTGCCAGATGGGCCAGTTGTTATTTCCCCTGATGGACTTTTTCCTTCTCTCTTTCGAGAAGMapped 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|162190415|gb|FC365637.1|FC365637EST: CAATCTCTCAGGCATATTTGACGCGCCAGTTTCTAGTTAACTTAAAGCAG GATGGTGAAGCAC
genomic: CAATCTCTCAGGCATATTTGACGCGCCAGTTTCTAGTTAACTTAAAGCAGgtgcgctatt ... gttattgcagGATGGTGAAGCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgtaaagaggtcttgaatattataatttcatcacaatttctgttattgcagGATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAG
tttctgtt CT-rich tract
ttgaatattataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgctatttgttttaaaataataattcaaaacagccgactttagactgattctgaagaaattttcttgttttcatgtagagtgatttggaggtcaactttccaccttgacctatgtctatagctacttgttgtaaagaggtcttgaatattataatttcatcacaatttctgttattgcagGATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA