Sequence
atgc intronic sequence ATGC exonic sequencegttagattatgcgatcttcctctctcatattcgtactttcatgttctttgctcaatgtatttatcatcttcaattgatatgcagCAAACAAACACAGCAGACATGTTGGATCTTGCGGTTCAATACATCAAGGACCTGCAAGAACAAGTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G51140.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G51140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g31300.1 (Oryza sativa), 3'ss of exon 3
-----------gttagattatgc---gatcttcctctctcatattcgtact--ttcatgttctttgc-tcaatgtatttatcatcttcaattgatatgcagCAAACAAACACAGCAGACATGTTGGATCTTGCGGTTCAATACATCAAGGACCTGCAAGAACAAGTGAAG
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aaaaaaaattactaacactgtactccagtgtgagctactactactagtactagctgatgagctgaccgtttgtgaatttgg-gttttggttttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAGCTCCAGAAGCAGGTCAAG
upper sequence: AT1G51140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g31300.2 (Oryza sativa), 3'ss of exon 3
-----------gttagattatg---cgatcttcctctctcatattcgtact--ttcatgttctttgc-tcaatgtatttatcatcttcaattgatatgcagCAAACAAACACAGCAGACATGTTGGATCTTGCGGTTCAATACATCAAGGACCTGCAAGAACAAGTGAAG
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aaaaaaaattactaacactgtactccagtgtgagctactactactagtactagctgatgagctgaccgtttgtgaatttgg-gttttggttttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAGCTCCAGAAGCAG------
upper sequence: AT1G51140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G05930.1 (Glycine max), 3'ss of exon 5
--------------------------gttagattatgcgatcttcctctctcatattcgtactttcatgttctttgc-tcaatgtatttatcat-cttcaattgatatgcagCAAACAAACACAGCAGACATGTTGGATCTTGCGGTTCAATACATCAAGGACCTGCAAGAACAAGTGAAG
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gtaattacgtttttgacttgttgcacactagcacacacatacgtcaccttttatgtgagaaaaattgtggaggaggccttgacacaccaacgttgttttcctctctttgcagCAAACAAACACAGCAGACATGTTGGACTTGGCTGTTGAGTACATTAAAGACCTTCAAAACCAAGTTGAG
upper sequence: AT1G51140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G13960.2 (Glycine max), 3'ss of exon 5
--------------------------gttagattatgcgatcttcctctctc----atattcgtactttcatgttctttgc-tcaatgtatttatcatcttcaattgatatgcagCAAACAAACACAGCAGACATGTTGGATCTTGCGGTTCAATACATCAAGGACCTGCAAGAACAAGTGAAG
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gtaatgaagtttttgacttgttgcacactagcacacacatacgtcaccttttaattatgtgtgaaaaattgtggaggaggccttgacaccaacgttgttttcctctctt-tgcagCAAACAAACACAGCTGACATGTTGGACTTGGCTGTTGAGTACATTAAAGACCTTCAAAACCAAGTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgtactttcatgttctttgctcaatgtatttatcatcttcaattgatatgcagCAAACAAACACAGCAGACATGTTGGATCTTGCGGTTCAATACATCAAGGACCTGCAAGAACAAGTGAAG
aattgat putative branch site (score: 4)
aatgtatttatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagattatgcgatcttcctctctcatattcgtactttcatgttctttgctcaatgtatttatcatcttcaattgatatgcagCAAACAAACACAGCAGACATGTTGGATCTTGCGGTTCAATACATCAAGGACCTGCAAGAACAAGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC