Sequence
atgc intronic sequence ATGC exonic sequencegtatacatatgcttcattattcagttttagtttttggaatcactgagatacaagtgacgctcagtttctttaactaacacatatttgttacattattcagACAAACCAGTGATCCTCAGAGTGGGTTTGCGACTGTTGAGAAGGATGTTCCTGGAAGCTTAACACCAATGCTTGGTGACAGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16780.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16780.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G24660.1 (Glycine max), 3'ss of exon 11
gtatacatatgcttcattattcagttttagtttttggaatcactgagatacaagtgacgctcagtttctttaacta-acacatatttgttacattatt--cagACAAACCAGTGATCCTCAGAGTGGGTTTGCGACTGTTGAGAAGGATGTTCCTGGAAGCTTAACACCAATGCTTGGTGACAGAAAG
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---aatatagcaagcctggcttctgtgtagtttcttctatcttctcttccttccttttgcttagttgatataccaatgtatgtgactgtttttctattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCCTGGGGGCTTGACACCTATGCTTGGTGATCGAAAG
upper sequence: AT5G16780.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G34600.1 (Glycine max), 3'ss of exon 11
gtatacatatgcttcattattcagttttagtttttggaatcactgagatacaagtgacgctcagtttctttaactaacacatatttgttacattatt--cagACAAACCAGTGATCCTCAGAGTGGGTTTGCGACTGTTGAGAAGGATGTTCCTGGAAGCTTAACACCAATGCTTGGTGACAGAAAG
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ataaatatagcaagcatggctctgtgt-agtttcttctatcttctcttctttccttttgtttagttgatata-ccaatgtatgtgactttttttattggcagACAAACTAGTGACCCAAAAAGTGGTTTTGCAACTGTTGAGAAGGATCTTCCTGGGGGCTTGACACCTATGCTTGGTGATCGAAAG
upper sequence: AT5G16780.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv11s0078g00440.t01 (Vitis vinifera), 3'ss of exon 11
-----gtatacatatgcttcattattcagt--tttagtttttggaatcactgagatacaagtgacgctcagtttctttaactaacacatatttgttacattattcagACAAACCAGTGATCCTCAGAGTGGGTTTGCGACTGTTGAGAAGGATGTTCCTGGAAGCTTAACACCAATGCTTGGTGACAGAAAG
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aaatcttaggattatggcctgttgttacataatttgctttcctgtattaatgtactcgaa-------tttgtttgctcatccttttcatatgttctgttggttccagCCAAACTAGTGATCCCAGAAGTGGTTTTGCTACAGTTGAGAAGGATGTCCCTGGGAGCTTAACACCCATGCTTGGCGATAGAAAGMapped 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|124845456|gb|EH929893.1|EH929893EST: CATGTCAAACCAGG ACAAACCAGTGATCCTCAGAGTGGGTTTGCGACTGTTGAGAAGGATGTTCC
genomic: CATGTCAAACCAGGgtatacatat ... cattattcagACAAACCAGTGATCCTCAGAGTGGGTTTGCGACTGTTGAGAAGGATGTTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatacaagtgacgctcagtttctttaactaacacatatttgttacattattcagACAAACCAGTGATCCTCAGAGTGGGTTTGCGACTGTTGAGAAGGATGTTCCTGGAAGCTTAACACCAATGCTTGGTGACAGAAAG
aactaac putative branch site (score: 1)
atatttgttacattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacatatgcttcattattcagttttagtttttggaatcactgagatacaagtgacgctcagtttctttaactaacacatatttgttacattattcagACAAACCAGTGATCCTCAGAGTGGGTTTGCGACTGTTGAGAAGGATGTTCCTGGAAGCTTAACACCAATGCTTGGTGACAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG