Sequence
atgc intronic sequence ATGC exonic sequence...gttaataattcattgatttgtcatctaaattggtttcatgaagttgtttttgcaaagagaagtaatcaattgagtttaaattgattttttctgtttgcagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
gttaataattcattgatttgtcatctaaattggtttcatgaagttgtttttgcaaagagaagtaatcaattgagtttaa-attgatttttt--ctgtttg-cagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG
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----atgctttgctggcctatgctatctattaaattgatttatgtattgcattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG
upper sequence: AT4G39100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G097726_T02 (Zea mays), 3'ss of exon 2
gttaataattcattgatttgtcatctaaattggtttcatgaagttgtttttgcaaagagaagtaatcaattgagtttaaattgattttttctgtttg---cagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG
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atagatggaacttt--ttttacttgtatatgtatttcttaaatctgaatcatcatttttacttgttttattcc-tctaatctcttctgtaaaacatgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG
upper sequence: AT4G39100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G01180.2 (Glycine max), 3'ss of exon 1
--gttaataattcattgatttgtcatctaaattggtttcatgaagttgtttttgcaaagagaagtaatcaattgagtttaaattgatttt--ttctgtttgcagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG
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aaaatggtaagtagcagcttt-ttgttagaatcgagaagctttgg--gatcttatgtagattctgactcgtgtga-tgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG
upper sequence: AT4G39100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
gttaata-attcattgatttgtcatctaaattggtttcatgaagt-tgtttttgcaaagagaagtaatcaattgagtttaaattgattttttctgtttgcagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG
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atatatatatatatatatatat-atatatatca-tcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
upper sequence: AT4G39100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
gttaataattcattgatttgtcatctaaattggtttcatgaagttgttt-ttgcaaagagaag--taatcaattgagtttaaattgattttttctgtttgcagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG
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tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgttctctgactgttc---tgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTGMapped 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|125096676|gb|EL153393.1|EL153393EST: ATCCTGGCAGAGTCACCGT GTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATG
genomic: ATCCTGACAGAGTCACCGTgtatgtgttc ... ctgtttgcagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATG
EST:
gi|125029879|gb|EL102148.1|EL102148EST: TGACAGAGTCACCGT GTTCTGCAAGTGTGAGATGCCGTATAACCCAG
genomic: TGACAGAGTCACCGTgtatgtgttc ... ctgtttgcagGTTCTGCAAGTGTGAGATGCCGTATAACCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttttgcaaagagaagtaatcaattgagtttaaattgattttttctgtttgcagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG
aattgat putative branch site (score: 4)
ttttttctgtttgc CT-rich tract
taatcaattgagttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaataattcattgatttgtcatctaaattggtttcatgaagttgtttttgcaaagagaagtaatcaattgagtttaaattgattttttctgtttgcagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG