Sequence
atgc intronic sequence ATGC exonic sequencegtattatcctctttggacctttgttctcgctagcagagtgctcattgatacttattatcagtgacagataaaatcaattatcattattaatcttcacctatgcagATTCGCAAAGAAAAAGCTATCTATCACACCTTGAACATGCTTAGTCTTGATGTGACTAAGAAGTGCCTTGTGGGTGAAGGCTGGAGTCCTGTCTTTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21410.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os10g10500.1 (Oryza sativa), 3'ss of exon 8
---------------------------------gtattatcctctttggacctttgttct-cgctagcagagtg-ctcattgatacttattatcagtgacagataaaatcaattatcattattaatctt---cacctatgc-agATTCGCAAAGAAAAAGCTATCTATCACACCTTGAACATGCTTAGTCTTGATGTGACTAAGAAGTGCCTTGTGGGTGAAGGCTGGAGTCCTGTCTTTGCAG
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gtaagcttgtattattcaagatgttttctgtaaattccctaccccacaaattttcaacctatactatttgaataacttttacgtctgtatattttcttttgcttgaatttaagttcttttgtgttttttatacaaatgtgccagGTAAAGAAAGAAAAAGCTATTTACCACACATTAAACATGTTGAGTCTTGATGTGACAAAGAAATGCTTGGTTGCTGAGGGATGGAGTCCGGTGTTTGCAA
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 8
--gtattatcctctttggacctttgttctcgctagcagagtgctcattgat--acttatta--tcagtg--acagataaa-atcaattatcattattaatcttcaccta-tgcagATTCGCAAAGAAAAAGCTATCTATCACACCTTGAACATGCTTAGTCTTGATGTGACTAAGAAGTGCCTTGTGGGTGAAGGCTGGAGTCCTGTCTTTGCAG
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gtaagctatcctcttatgtgataaattccatatgttagaaaattccgaaatccaccagtcaggtcattatttcagttctatatatatgatactaattagcatacaaatgctccagGCAAATAAGGAAAAAATAATTTACCACACTTTGAACATGTTGAGTGTTGATGTGACAAAGAAATGCTTAGTTGGTGAGGGCTGGAGTCCAGTTTTTGCAA
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 8
-----------gtattatcctctttggacctttg----ttctcgcta-gcagagtgctcattgat--acttattat-cagtgacagataaaa---tcaattatcattattaatcttca---cctatg---cagATTCGCAAAGAAAAAGCTATCTATCACACCTTGAACATGCTTAGTCTTGATGTGACTAAGAAGTGCCTTGTGGGTGAAGGCTGGAGTCCTGTCTTTGCAG
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gtaagcttcacttgttttctccatgaagttgatgaaattttacgttttgaagtttacttatagctttactttgcattctatctcatatcacagttttcattatcattattaaatttcaaaatcaatgctacagGTCAAAAAGGAAAAGGCAATTTATCACACCTTGAACATGCTAAGTGTTGATGTTACGAAGAAATGTTTAGTTGCTGAGGGCTGGAGTCCAATTTTTGCAA
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G12120.1 (Glycine max), 3'ss of exon 8
gtattatcctctttggacctttgttctcgctagcagagtgctcattgatacttattatcagtgacagataaaatcaattatcattattaatcttcacctatgcagATTCGCAAAGAAAAAGCTATCTATCACACCTTGAACATGCTTAGTCTTGATGTGACTAAGAAGTGCCTTGTGGGTGAAGGCTGGAGTCCTGTCTTTGCAG
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--atttccattctcaagtatacaattt-acttgtagattgat-atatttttctattggtcttaatgtttaatttttcttgacaatattc-tttaaattcatgaagGTGAGGAAGGAGAAATCTATTCATCATACCCTGAACATGCTGAGCCTTGATGTGACAAAAAAATGTCTTGTGGCTGAGGGGTGGAGTCCTGTTTTTGCAA
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G04330.1 (Glycine max), 3'ss of exon 8
gtattatcctctttggacctttgttctcgctagcagagtg-ctcattgatacttattatcagtgacagataaaatcaattatcattattaatcttcacctatgcagATTCGCAAAGAAAAAGCTATCTATCACACCTTGAACATGCTTAGTCTTGATGTGACTAAGAAGTGCCTTGTGGGTGAAGGCTGGAGTCCTGTCTTTGCAG
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--attatcattctcaagtatacaattt-acttgtagattaatttatt--tttctattggtcttaatgtttaatttttcttgactatattc-tttaaattcatgaagGTGAGGAAGGAGAAATCTATTCATCATACCCTGAACATGCTGAGCCTTGATGTAACAAAAAAATGTCTTGTGGCTGAGGGGTGGAGTCCTGTTTTTGCAAMapped 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|116483494|gb|EG526086.1|EG526086EST: ACATTCTTTTAGAGACCATTGGAGATAAGTTTGAGCAATGGAACCTCAAG ATTCGCAAAGAAAAAGCTATCTATCACACCTTGAACATGCTTAGTCTTGAT
genomic: ACATTCTTTTAGAGACCATTGGAGATAAGTTTGAGCAATGGAACCTCAAGgtattatcct ... acctatgcagATTCGCAAAGAAAAAGCTATCTATCACACCTTGAACATGCTTAGTCTTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttattatcagtgacagataaaatcaattatcattattaatcttcacctatgcagATTCGCAAAGAAAAAGCTATCTATCACACCTTGAACATGCTTAGTCTTGATGTGACTAAGAAGTGCCTTGTGGGTGAAGGCTGGAGTCCTGTCTTTGCAG
tattaat putative branch site (score: 2)
tcttcacct CT-rich tract
agataaaatcaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattatcctctttggacctttgttctcgctagcagagtgctcattgatacttattatcagtgacagataaaatcaattatcattattaatcttcacctatgcagATTCGCAAAGAAAAAGCTATCTATCACACCTTGAACATGCTTAGTCTTGATGTGACTAAGAAGTGCCTTGTGGGTGAAGGCTGGAGTCCTGTCTTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA