Sequence
atgc intronic sequence ATGC exonic sequencegtacatttctacaagtccttctcgcatagctctcttattgcgctccctctcttaatggttttactcatgtcacaaactcacaatatatgtgtatttgcagGTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGCTTGTTAGCTAGAATGATGGCTGCTACTATGTACTTTAACCAAATCGAAGATCTTATGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G53310.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
gtacatttctacaagtccttctcgcatagctctcttattgcgctccctctcttaatggttttactcatgtcacaaactcacaatatatgtgtatttgcagGTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGCTTGTTAGCTAGAATGATGGCTGCTACTATGTACTTTAACCAAATCGAAGATCTTATGTT
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-------------------gtatgcaaaggatggcttttgacttctgtatagttcagttcttgtgcatttaataattttgtgcattgcaccaattt--agGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
upper sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
gtacat----ttctacaagtccttctcgcatagctctcttattgcgctccctctcttaatggttttactcatgtcacaaactcaca-atatatgtgtatttg---------cagGTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGCTTGTTAGCTAGAATGATGGCTGCTACTATGTACTTTAACCAAATCGAAGATCTTATGTT
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gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
upper sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 4
gtacatttctacaagtccttctcgcatagc-tctcttattgcgctccctctctta-atggt--tttactcatgtcacaaactcacaatatatgtgtatttgcagGTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGCTTGTTAGCTAGAATGATGGCTGCTACTATGTACTTTAACCAAATCGAAGATCTTATGTT
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--aaaccaatggaaattttaagtaaatggaatttcttatttaaaaccacttctaagattatgatgtattggtggcttaatgttgctttg-atgtggatg-gcagGAAACCCCAGGGTAACACCTGAAGTTACAAGGGATGTATGCTTATTGGCCAGAATGATGGCTGCTAACTTGTATTATTCTCAGATAGAGGACCTTATGTTMapped 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|164078294|gb|ES000408.1|ES000408EST: TAATGCTCCATTGATTCAGTTCTCTTCTTGGATGGGTGGTGATCGTGACG GTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGC
genomic: TAATGCTCCATTGATTCAGTTCTCTTCTTGGATGGGTGGTGATCGTGACGgtacatttct ... gtatttgcagGTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGC
EST:
gi|124942687|gb|EL018934.1|EL018934EST: TCTTGGATGGGTGGTGATCGTGACG GTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGCTTGTTAGCTA
genomic: TCTTGGATGGGTGGTGATCGTGACGgtacatttct ... gtatttgcagGTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGCTTGTTAGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctctcttaatggttttactcatgtcacaaactcacaatatatgtgtatttgcagGTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGCTTGTTAGCTAGAATGATGGCTGCTACTATGTACTTTAACCAAATCGAAGATCTTATGTT
aactcac putative branch site (score: 2)
aatatatgtgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatttctacaagtccttctcgcatagctctcttattgcgctccctctcttaatggttttactcatgtcacaaactcacaatatatgtgtatttgcagGTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGCTTGTTAGCTAGAATGATGGCTGCTACTATGTACTTTAACCAAATCGAAGATCTTATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA