Sequence
atgc intronic sequence ATGC exonic sequencegtaattttcccttaacactactctatgaaactggatacaacatttgtgtgcttattactttcatatgaagctcttgtctttgtcacattattagctctaggctgctacttgttaatagcgttgtgactgattgattgcttataaacaaatatgtgtttggggttgttgtagATTTGGACTTCATGTTCCATATGTTCTTTCTCGCACGATACTGCAAACTCCTTGAAGAAAACTCATTCAGGGGAAAGACTGCTGATTTCCTATACATGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G04860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 2
gtaattttcccttaacactactctatgaaactggatacaacatttgtgtgcttattactttcatatgaagctcttgtctttgtcacattattagctctaggctgctacttgttaatagcgttgtgactgattgattgcttataaacaaatatgtgtttggggttgttgtagATTTGGACTTCATGTTCCATATGTTCTTTCTCGCACGATACTGCAAACTCCTTGAAGAAAACTCATTCAGGGGAAAGACTGCTGATTTCCTATACATGCT
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-----------------------------------------------------------agaacatgtaagcgctgttattctagcattatt-------gaataatttttatgcataa---tttaatccctttact-cttattcctgaatccatcttttgttgt-ttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT
upper sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G082976_T01 (Zea mays), 3'ss of exon 2
gtaattttcccttaacactactctatgaaactggatacaacatttgtgtgcttattactttcatatgaagctcttgtctttgtcacattattagctctaggctgc-tacttgttaatagcgttgtgactgattgattgcttataa-acaaatatg-tgtttggggttgttgtagATTTGGACTTCATGTTCCATATGTTCTTTCTCGCACGATACTGCAAACTCCTTGAAGAAAACTCATTCAGGGGAAAGACTGCTGATTTCCTATACATGCT
| | | | || |||| |||| ||| | || ||| | || | | || || | ||||||| | ||| | | | | || || ||||||||| || ||||||| ||||| |||||||||||||||||||| || || || || |||||||| || |||| ||||| || || | ||||||||
-------------------------------------------------------------------------tcgctccagacttataattactattaggttgcatgctgtttatttgcatctcaagtgcttcacc-cttataataaaaacttactctctttcttttttccagATTTGGATTTTCTGTTCCACATGTTTTTTCTCGCACGATACTGCAAGCTTCTGGAGGAGAACTCATTTAGAGGAAGAACTGCCGACTTTTTTTACATGCT
upper sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G112609_T01 (Zea mays), 3'ss of exon 2
gtaattttcccttaacactactctatgaaactggatacaacatttgtgtgcttattactttcatatgaagctcttgtctttgtcacattattagctctag-gctgct-acttgttaatagcgttgtgactgattgattgcttataaacaaatatgtgtttggggttgttgtagATTTGGACTTCATGTTCCATATGTTCTTTCTCGCACGATACTGCAAACTCCTTGAAGAAAACTCATTCAGGGGAAAGACTGCTGATTTCCTATACATGCT
| | | | || |||| ||| |||| ||| ||| | || || | || || | ||||||| || | | | || ||||||||| || | ||||| ||||||||||| ||||| |||||||| || || || ||||||||||| || |||| |||||||| || | ||||||||
----------------------------------------------------------------------gcatcattccagacttataattactgttagcattgcttactgtttatttgcatttcaagtgcttcacc-cttataa-tgaagacctactcttt-ttcccccagATTTGGATTTTCTATTCCACATGTTCTTTCTTGCACGGTACTGCAAGCTTCTGGAGGAAAACTCATTTAGAGGAAGAACTGCTGACTTTTTTTACATGCT
upper sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G11350.2 (Glycine max), 3'ss of exon 2
gtaattttcccttaacactactctatgaaactggatacaacatttgtgtgcttattactttcatatgaagctcttgtctttg-tcacattattagctc-taggctgctacttgttaatagcgttgtgactgattgattgcttataaacaaatatgtgtttggggttgttgtagATTTGGACTTCATGTTCCATATGTTCTTTCTCGCACGATACTGCAAACTCCTTGAAGAAAACTCATTCAGGGGAAAGACTGCTGATTTCCTATACATGCT
| || |||||| || | || || || | | || | || | | | ||||| || | | | | ||| | || | | ||| ||||| ||| |||| |||||||| ||||| || || |||||||| || ||||| || ||||| |||||||| | ||||||||||||| | ||||||||
----------------------------------------------------------------------atattctctttgctctctttgtttcatcatcgtttgatgtttaattagaaaattgtgc---atcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCCCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT
upper sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G27600.1 (Glycine max), 3'ss of exon 2
gtaattttcccttaacactactctatgaaactggatacaacatttgtgtgcttattactttcatatgaagctcttgtctttgtcacattattagctctaggctgctacttgttaatagcgttgtgactgattgattgcttataaacaaatatgtgtttggggttgttgtagATTTGGACTTCATGTTCCATATGTTCTTTCTCGCACGATACTGCAAACTCCTTGAAGAAAACTCATTCAGGGGAAAGACTGCTGATTTCCTATACATGCT
| | ||| | || | || || | || || || | | | ||| || || | | | | ||| | || | | ||| ||||| ||| |||| |||||||| ||||| || || |||||||| || ||||| || ||||| |||||||| | ||||||||||||| | ||||||||
-----------------------------------------------------------------aataacccttattcttatttgtttcataatcgt---ttgatatttaattagaaagttatgc---atcttctaaatttgacatggtattttcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcgttgtgactgattgattgcttataaacaaatatgtgtttggggttgttgtagATTTGGACTTCATGTTCCATATGTTCTTTCTCGCACGATACTGCAAACTCCTTGAAGAAAACTCATTCAGGGGAAAGACTGCTGATTTCCTATACATGCT
ttataaacaaatatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattttcccttaacactactctatgaaactggatacaacatttgtgtgcttattactttcatatgaagctcttgtctttgtcacattattagctctaggctgctacttgttaatagcgttgtgactgattgattgcttataaacaaatatgtgtttggggttgttgtagATTTGGACTTCATGTTCCATATGTTCTTTCTCGCACGATACTGCAAACTCCTTGAAGAAAACTCATTCAGGGGAAAGACTGCTGATTTCCTATACATGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT