Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaatgagtcatttttgctagcttatatatctgctgtgttgtcacctgatcattatagcaataatatgaatttactcaaattaatttttgtgagaaagagcagTTCATCTATGATTTACCTGCAAGACTGCAAAAATGTATCAAGTCAGAAGCCTATGGCGATGCTGTCAGGTTCTATACTGGAGCAATGCCAATTCTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02030.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G023858_T03 (Zea mays), 3'ss of exon 4
gtatgtaatgagtcatttttgctagcttatatatctgctgt-gttgtcacctgatcatta-tagcaataatatgaatttactcaaattaatttttgtgagaaagagcagTTCATCTATGATTTACCTGCAAGACTGCAAAAATGTATCAAGTCAGAAGCCTATGGCGATGCTGTCAGGTTCTATACTGGAGCAATGCCAATTCTCAAG
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actgccagtgaattctaataactaactaactaactaaatgtaggtgcagaaaaaagaaaacttttgataaaatg--ttagtttcaatcaacttctttt-------gcagTTCATATATGACCTTCCAACTCGTCTTAACAAATGCATCAAGACAGAAGCATATGCAGATGCTGTCAGGTTTTTTACTGGAGCAAAACCTATTTTTGAG
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G01610.1 (Glycine max), 3'ss of exon 4
--------------------------gtatg-taatgagtcatttttgctagcttatatatctgct---gtgttgtcacctg---atcat-tatagcaataatatgaatttactcaaattaatttttgtgagaaagagcagTTCATCTATGATTTACCTGCAAGACTGCAAAAATGTATCAAGTCAGAAGCCTATGGCGATGCTGTCAGGTTCTATACTGGAGCAATGCCAATTCTCAAG
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gtattagagcaatcatgcatgtttctttattctggcccatcatcatttcaatattgtgttcccgcattggtgatatgagttgtgagtcttctgtggaagtggtatatgactgacatactttttacctttgtcgaagagtagTTCATATATGATCTCCCCGATAGACTAGGCAAGTGCATCAAGTCGGAGGCCTATGCAGATGCAGTCAGGTTTTACATTGGAGCAATGCCAATTTTTAAG
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G01660.1 (Glycine max), 3'ss of exon 4
----------------------------------------------gtatgtaatgagtcatttttgctagcttatat-atctgctgtgttgtcacctgatcattatagcaataatatgaatttactcaaattaatttttg---tgagaaagagcagTTCATCTATGATTTACCTGCAAGACTGCAAAAATGTATCAAGTCAGAAGCCTATGGCGATGCTGTCAGGTTCTATACTGGAGCAATGCCAATTCTCAAG
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gtattaattattaaagcaatcatgcatgtttctttattccggctttgcat-cactgaaatatttatgtttccatacttgacttagtggtatgacttctgagtctttt-gtggaagtg-gaatatgactgacatactttttacctttgttgaaagtagTTCATATATGACCTACCCGATAGACTAAGCAAGTGCATCAAGTCGGAGGCCTATGCAGATGCAGTCAGGTTTTACATTGGAGCAATGCCAATTTTTAAG
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0005g01440.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtaatgagtcatttttgctagcttatatatctgct--gtgttgtcacctgatcattatagcaataatatgaatttactcaaattaatttttgtgagaaagagcagTTCATCTATGATTTACCTGCAAGACTGCAAAAATGTATCAAGTCAGAAGCCTATGGCGATGCTGTCAGGTTCTATACTGGAGCAATGCCAATTCTCAAG
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ggtcggaaataatcttatttgatgttcaatactttatgtaagttttggtgtttggccat-gtatgagttacacagatttcatc--------ttctgtggaaaagagcagTTCATATATGATCTACCTACTAGGCTTGGAAAATGTATTAAATCCGAAGCTTATGCTGATGCAGTCAGGTTTTATACTGGAGCCATGCCGATTTTTGAGMapped 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|19876508|gb|AU237339.1|AU237339EST: AACATATAGAGAAACTGCACCGGACTCGTAATCTTCTTCGTAAAGGTCAG TTCATCTATGATTTACCTGCAAGACTGCAAAA-TGTATCAAGTCAGAAGCC
genomic: AACATATAGAGAAACTGCACCGGACTCGTAATCTTCTTCGTAAAGTTCAGgtatgtaatg ... gaaagagcagTTCATCTATGATTTACCTGCAAGACTGCAAAAATGTATCAAGTCAGAAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcattatagcaataatatgaatttactcaaattaatttttgtgagaaagagcagTTCATCTATGATTTACCTGCAAGACTGCAAAAATGTATCAAGTCAGAAGCCTATGGCGATGCTGTCAGGTTCTATACTGGAGCAATGCCAATTCTCAAG
aattaat putative branch site (score: 3)
tatagcaataatatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaatgagtcatttttgctagcttatatatctgctgtgttgtcacctgatcattatagcaataatatgaatttactcaaattaatttttgtgagaaagagcagTTCATCTATGATTTACCTGCAAGACTGCAAAAATGTATCAAGTCAGAAGCCTATGGCGATGCTGTCAGGTTCTATACTGGAGCAATGCCAATTCTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA