Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtataaccaaattattcgtttactttaaataattaattagacgatagtgtaacatataaactcatgtgtaaatgcatgagtttataatttgtgaaaacctataattgatttttttttattaatataacagACATAGATGGACTGGAAGATACGAAGCTCATCTATGGGATAATAGTTGCCGAAGAGAAGGCCAAAGCAGAAAAGGAAGACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57390.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G00950.1 (Glycine max), 3'ss of exon 2
gtgcgtataaccaaattattcgtttactttaaataattaattagacgatagtgtaacatataaactcatgtgtaaatgcatgagtttataatttgtgaaaacctataattgatttttttttattaatataacagACATAGATGGACTGGAAGATACGAAGCTCATCTATGGGATAATAGTTGCCGAAGAGAAGGCCAAAGCAGAAAAGGAAGACAAG
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--gtatcttattaatcatcgccaccaccaccaccaccatcttttatcat--tataatatatatatatatatatatatatatatatatata-tatatatatttatttatctggtcttgtttc-ttatttt--cagACATAGATGGACGGGAAGATACGAAGCTCATCTATGGGACAATAGTTGTAGAAGAGAAGGCCAAAGCAGGAAAGGAAGACAAG
upper sequence: AT5G57390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G07010.1 (Glycine max), 3'ss of exon 2
gtgcgtataaccaaattattcgtttactttaaataattaattagacgatagtgtaacatataaactcatgtgtaaatgcatgagtttataatttgtgaaaacctataattgatttttttttattaata--taacagACATAGATGGACTGGAAGATACGAAGCTCATCTATGGGATAATAGTTGCCGAAGAGAAGGCCAAAGCAGAAAAGGAAGACAAG
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-----------------------------------------------gta-tcttattcatgaccaccaccttttat-catcataatataatattagtaattattttatttatctgattctgtttcttattttcagACATAGATGGACTGGGAGATACGAAGCTCATCTATGGGACAATAGTTGCAGAAGGGAAGGTCAAAGCAGGAAAGGAAGGCAAG
upper sequence: AT5G57390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0052g00840.t01 (Vitis vinifera), 3'ss of exon 2
gtgcgtataaccaaattattcgtttactttaaataattaattagacgatagtgtaacatataaactcatgtgtaaatgc---atgagtttataatttgtgaaaac-----ctataattgatttttttttattaatataa-cagACATAGATGGACTGGAAGATACGAAGCTCATCTATGGGATAATAGTTGCCGAAGAGAAGGCCAAAGCAGAAAAGGAAGACAAG
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---------------------------gtgatgtgaaaaat--gatgatctccttccctgaaaacctcggggaaaattttttattattatttttcttctgaaaataataataataataaattatctcaaatttatattttcagACATAGATGGACAGGGAGATATGAAGCCCATCTCTGGGACAACAGCTGCAGAAGAGAAGGACAGAGCCGGAAGGGACGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgagtttataatttgtgaaaacctataattgatttttttttattaatataacagACATAGATGGACTGGAAGATACGAAGCTCATCTATGGGATAATAGTTGCCGAAGAGAAGGCCAAAGCAGAAAAGGAAGACAAG
tattaat putative branch site (score: 2)
tttataatttgtgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtataaccaaattattcgtttactttaaataattaattagacgatagtgtaacatataaactcatgtgtaaatgcatgagtttataatttgtgaaaacctataattgatttttttttattaatataacagACATAGATGGACTGGAAGATACGAAGCTCATCTATGGGATAATAGTTGCCGAAGAGAAGGCCAAAGCAGAAAAGGAAGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA