Sequence
atgc intronic sequence ATGC exonic sequencegtgaattttgaagcaaacaaattgtaacccgattatctttcatgttgtactcttcagacagactctgattttactggtctgaattttttggatattatagGTTGCTTTTTGGAAGTGGATCACACCTAAGATGCTGGGACTGGTCACACAAACTTCTGTGTATCATTGGTCAATTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11130.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 3
gtgaattttgaagcaaacaaattgtaacccgattatctttcatgttgtactcttcagacagactctgattttac-tggtctgaattttttggatattatagGTTGCTTTTTGGAAGTGGATCACACCTAAGATGCTGGGACTGGTCACACAAACTTCTGTGTATCATTGGTCAATTGAAG
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gtaactgtt-atgcacgagtatacaaacactattaagcg--atggttgatgatgaaaact--ctattaatccacgtggaatgctctaatttcatgt-gcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 3
--gtgaattttga-----agcaaacaaattgtaaccc---gattatcttt-catgttgtactcttcagacagactctg-attttactggtctgaatttt-ttggatattatagGTTGCTTTTTGGAAGTGGATCACACCTAAGATGCTGGGACTGGTCACACAAACTTCTGTGTATCATTGGTCAATTGAAG
| ||| |||| |||| || | | ||| || ||| | | | || | | | | | || || || || ||| || |||| ||| ||| ||||||||||| || || ||||||||||| |||||||| || || || || |||||||||||||| ||||
gtgagaactttgttctttagcatttctgttacatttcttgagctattttgacatcctacattgttaacattgctattacagttagcttaactatgccttgttgtttaaaatagATTGTTTTCTGGAAGTGGATTACCCCAAAGATGCTGGGCCTGGTCACGCAGACCTCAGTATATCATTGGTCAATCGAAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgaattttgaagcaaacaaattgtaac-------ccgattatc--tttcatgttgtactcttca--gacagactctgattttactggtctgaattttttggatattat-agGTTGCTTTTTGGAAGTGGATCACACCTAAGATGCTGGGACTGGTCACACAAACTTCTGTGTATCATTGGTCAATTGAAG
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gtgagtaaccatacatgtcactggtttcggtgttgctgatgattgttttaccatgggagtttccaatgacaagaaataaattttctacccttaatacggtatatgttatcagGTAGTTTTTTGGAAGTGGATTACACCGAGGTTGCTAGGACTCGTGACACAAACTTCAGTTTATCACTGGACTATTGAAGMapped 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|19877198|gb|AU238029.1|AU238029EST: TTAACATTGAAGCAAAGGCAAAGTTGAAGTCACATCAGATGCCTGAGCAG GTTGCTTTTTGGAAGTGGATCACACCTAAGATGCTGGGACTGGTCACACAA
genomic: TTAACATTGAAGCAAAGGCAAAGTTGAAGTCACATCAGATGCCTGAGCAGgtgaattttg ... gatattatagGTTGCTTTTTGGAAGTGGATCACACCTAAGATGCTGGGACTGGTCACACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtactcttcagacagactctgattttactggtctgaattttttggatattatagGTTGCTTTTTGGAAGTGGATCACACCTAAGATGCTGGGACTGGTCACACAAACTTCTGTGTATCATTGGTCAATTGAAG
ctctgat putative branch site (score: 4)
aattttttggatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaattttgaagcaaacaaattgtaacccgattatctttcatgttgtactcttcagacagactctgattttactggtctgaattttttggatattatagGTTGCTTTTTGGAAGTGGATCACACCTAAGATGCTGGGACTGGTCACACAAACTTCTGTGTATCATTGGTCAATTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG