Sequence
atgc intronic sequence ATGC exonic sequencegtatgggtttatagtatccttgtgcaactcatttagtttttgctcctgtgtaaaatgcttattagcacgtgcagctacctcgttcatgaggggattagcctaaaaatgcagaatcttcatttccagaccatgagttatgtgtgtttgtctaaatttacagTCAGGTCTTCAGCGCTTGAGCGACTTCCCTCGACCTTTCTGGTTAGCCCTTTTTGTGGAGGGAACTCGCTTTACAGAAGCCAAACTTAAAGCCGCACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G57650.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g41900.1 (Oryza sativa), 3'ss of exon 6
gtatgggtttatagtatccttgtgcaactcatttagtttttgctcctgtgtaaaatgcttattagcacgtgcagctacctcgttcatgaggggattagcctaaaaatgcagaatcttcatttccagaccatgagttatgtgtgtttgtctaaatttacagTCAGGTCTTCAGCGCTTGAGCGACTTCCCTCGACCTTTCTGGTTAGCCCTTTTTGTGGAGGGAACTCGCTTTACAGAAGCCAAACTTAAAGCCGCACAAG
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--------------------------------------------------------------------------gtaacttttttacctcat--ctacacagtacacacataattctattgtttgttctttaactta-gtggtcttg-ctatgcttatagTGGGGCCTCCAAAGGTTGAAGGACTTCCCCAGACCATTTTGGCTAGCCCTTTTTGTTGAGGGCACTCGCTTTACTCCAGCAAAGCTTCTAGCAGCTCAGG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 4
gtatgggtttatagtatccttgtgcaactcatttagtttttgctcctgtgtaaaatgcttattagcacgtgcagctacctcgttcatgaggggattagcctaaaaatgcagaatcttcatttccagaccatgagttatgtgtgtttgtctaaatttacagTCAGGTCTTCAGCGCTTGAGCGACTTCCCTCGACCTTTCTGGTTAGCCCTTTTTGTGGAGGGAACTCGCTTTACAGAAGCCAAACTTAAAGCCGCACAAG
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------------------------------------------------------------------gtaactctccaccttacctatattggg--catcctagtttt-------cctttttttcacatagtgagctttttaattttgcata------cagTGGGGTCTCCAAAGGTTGAAAGACTTCCCTAGACCATTTTGGCTAGCTCTTTTTGTTGAGGGTACTCGCTTTACTCCAGCAAAGCTTCTCGCAGCTCAGG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 6
gtatgggtttatagtatccttgtgcaactcatttagtttttgctcctgtgtaaaatgcttattagcacgtgcagctacctcgttcatgaggggattagcctaaaaatgcagaatcttcatttccagaccatg-agttatgtgtgtttgtctaaatttacagTCAGGTCTTCAGCGCTTGAGCGACTTCCCTCGACCTTTCTGGTTAGCCCTTTTTGTGGAGGGAACTCGCTTTACAGAAGCCAAACTTAAAGCCGCACAAG
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---------------------gtactgctgcagcaaaaattttctgaatatgtactgtgtatgtgtgtgtaca---------tatatgcttgcacaaatccttatattcgagctgttcacatcgatctttttcaattttttatgacattgt--atctgcagTCAGGTCTTCTACGGTTAAAGGACTACCCTCAGCCTTTTTGGTTGGCTCTTTTTGTTGAGGGAACTCGCTTTACACAGGCAAAGCTTTTAGCAGCTCAAGMapped 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|124993043|gb|EL065312.1|EL065312EST: AGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG TCAGGTCTTCAGCGCTTGAGCGACTTCCCT
genomic: AGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAGgtatgggttt ... aaatttacagTCAGGTCTTCAGCGCTTGAGCGACTTCCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcagaatcttcatttccagaccatgagttatgtgtgtttgtctaaatttacagTCAGGTCTTCAGCGCTTGAGCGACTTCCCTCGACCTTTCTGGTTAGCCCTTTTTGTGGAGGGAACTCGCTTTACAGAAGCCAAACTTAAAGCCGCACAAG
gtctaaa putative branch site (score: 3)
tttgtctaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgggtttatagtatccttgtgcaactcatttagtttttgctcctgtgtaaaatgcttattagcacgtgcagctacctcgttcatgaggggattagcctaaaaatgcagaatcttcatttccagaccatgagttatgtgtgtttgtctaaatttacagTCAGGTCTTCAGCGCTTGAGCGACTTCCCTCGACCTTTCTGGTTAGCCCTTTTTGTGGAGGGAACTCGCTTTACAGAAGCCAAACTTAAAGCCGCACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC