Sequence
atgc intronic sequence ATGC exonic sequencegtctgcaagtataccttatatcggtgtctatagttgattataggaatcttcaatatgtaataattcttggttctttttcagTTTGGCAACCTTCCTTATGGTTTCCGGGCAAACACTTGGGTAGTTCCTCCGGTTGTTGCAGATAGTCCATCTACTTTTCCGTCACTTCCAGTGGAGGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28080.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G30000.1 (Glycine max), 3'ss of exon 6
gtctgcaagtataccttatatcggtgtctatagttgattataggaatcttcaatatgtaataattct-----tggttctttttcagTTTGGCAACCTTCCTTATGGTTTCCGGGCAAACACTTGGGTAGTTCCTCCGGTTGTTGCAGATAGTCCATCTACTTTTCCGTCACTTCCAGTGGAGGATG
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----gtaagtacttctcattataacttttcacattactttgctaattgtactggatgtttttaccattacagtggtgtcatttcagTTTGGCAATCTTCCTTACGGTTTTCGTGCAAACACATGGGTTGTCCCTCCAGTTGTTTCTGACAATCCATCAGTCTTTCTGCCACTTCCCATGGAAGATG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 5
gtctgcaagtataccttatatcggtgtctatagttgattataggaatcttcaatatgtaataattctt-----ggttctttttcagTTTGGCAACCTTCCTTATGGTTTCCGGGCAAACACTTGGGTAGTTCCTCCGGTTGTTGCAGATAGTCCATCTACTTTTCCGTCACTTCCAGTGGAGGATG
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----gtaagtacttctcattatgatttttcgcattactttgctaattgtgcagGATGTTTTTACCATTATAGTGGTGTCATTTCAGTTTGGCAATCTTCCTTACGGTTTTCGTGCAAACACATGGGTTGTCCCTCCAGTTGTTTCTGACAATC---------------------------------
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv11s0037g00840.t01 (Vitis vinifera), 3'ss of exon 8
gtctgcaagtataccttatatcggtgtctatagttgattataggaatcttcaatatgtaataattcttggttctttttcagTTTGGCAACCTTCCTTATGGTTTCCGGGCAAACACTTGGGTAGTTCCTCCGGTTGTTGCAGATAGTCCATCTACTTTTCCGTCACTTCCAGTGGAGGATG
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----gtcagtgtgatttgcacaaatcttcatacttaatcttcagagagatgattag-----aattgcatcccttttttcagTTTGGAAACCTTCCTTATGGTTTTCGTGCAAACACATGGGTTGTGCCACCAGTTATTGCTGATAATCCATCTCATTTTCCCCCACTACCCATTGAAGATG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------gtctgcaagtatac-cttatatcggtgtctatagttgattataggaatcttcaatatgtaataattcttggttctttttcagTTTGGCAACCTTCCTTATGGTTTCCGGGCAAACACTTGGGTAGTTCCTCCGGTTGTTGCAGATAGTCCATCTACTTTTCCGTCACTTCCAGTGGAGGATG
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gtatgacccgatatctgtccaatttgttatttgagggacccacgtgtaaacacttgctcagttgaatgaaattgaagagaatagtttctgacttgcc-ta--tctcgatt---tttcagTTTGGCAATCTTCCTTATGGCTTCCGATCCAACACATGGGTAGTTCCTCCAGTGGCAGCCGATGCCCCTTCGGAGTTTCCTCTGCTCCCCACTGAAGATAMapped 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|124779669|gb|EH869612.1|EH869612EST: GCTTATGACGCTCTTATGAAAGCTTTCATTGAGCACAATAAG TT-GGCAACCTTCCTTATGGTTTCCGGGCA
genomic: GCTTATGACGCTCTTATGAAAGCTTTCATTGAGCACAATAAGgtctgcaagt ... tctttttcagTTTGGCAACCTTCCTTATGGTTTCCGGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatagttgattataggaatcttcaatatgtaataattcttggttctttttcagTTTGGCAACCTTCCTTATGGTTTCCGGGCAAACACTTGGGTAGTTCCTCCGGTTGTTGCAGATAGTCCATCTACTTTTCCGTCACTTCCAGTGGAGGATG
agttgat putative branch site (score: 5)
ttcttggttctttttc putative PPT
aatcttcaatatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgcaagtataccttatatcggtgtctatagttgattataggaatcttcaatatgtaataattcttggttctttttcagTTTGGCAACCTTCCTTATGGTTTCCGGGCAAACACTTGGGTAGTTCCTCCGGTTGTTGCAGATAGTCCATCTACTTTTCCGTCACTTCCAGTGGAGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG