Sequence
atgc intronic sequence ATGC exonic sequence...tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54480.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os07g46555.1 (Oryza sativa), 3'ss of exon 1
tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcg--tactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
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-tgcttgattttgt-ccctgctaccatttattgcctgataatgtgacgctgtttatgtactttaaatgagctttttttagcatttcatttttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCATCCTCGACTGTGGTTGCGTGTTGAGAGGCCAATCAGAAATACAATAGA
upper sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G009021_T01 (Zea mays), 3'ss of exon 1
tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA-------------------------------
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----------------ttaacatatactgctgacgtgg---tttaaaatgaactgttttttttatcaatttcattgt------------tgaacctgcagataggtataacaccgccctcgtttgccacagATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGAGCCTGGAGTTTATCCAGATCTCGAGGCTGCT
upper sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G009021_T02 (Zea mays), 3'ss of exon 1
tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtactacagtctgtttcaatgctgttttgtgt--atctc-ttgt-gagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
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---ctggatgtcacatgttttttg-atagcatgccttaacatatactgctgacgtggtttaaaatgaactgttttttttatcaatttcattgttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGA
upper sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G21550.1 (Glycine max), 3'ss of exon 1
tttgaaaatttcgtattttgtttgtatgattgacttgggca------tttgttgcgtactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
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-cttaggcgctaatcctctcttaaaataattttctttgaaaaaataattaatagcatacagcagagcatttt----ctatcacaaa-gctgctattgagtttgcagATCGCTTTAATACCGCCCTCGTTTGCCACAGATGGAATTACTTGGCATGTCATCCTCGCTTGTGGCTTCGGGTTGATCGATCAGTTAAAGAGTTATCTGA
upper sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0139g00260.t01 (Vitis vinifera), 3'ss of exon 2
tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtac---tacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
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--agttcattctcgatactgctgttgcatctgagagatgttgttgccccatgcatatatgatatcatacagt-ctctgtcatggattgccattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGAMapped 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|125065136|gb|EL132478.1|EL132478EST: TGGTTGCCTTATGCATATCCTCAGCTTCCTATCTCCAATTCCAG ATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGC
genomic: TGGTTGCCTTATGCATATCCTCAGCTTCCTATCTCCAATTCCAGgtaaaattgg ... gagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcgtactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
tttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtactacagtctgtttcaatgctgttttgtgtatctcttgtgagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA
- - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg