Sequence
atgc intronic sequence ATGC exonic sequencegtacaatgaagattaagttagcttgttgttggttttggttttgtgctggagtgtcaaacaaatttctagttttcattctgttggccattaattgtgaaccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13060.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 3'ss of exon 2
gtacaatgaagattaagttagcttgttgttggttttggttttgtgctggagtgtcaaacaaatttctagttttcattctgttggccattaattgtgaaccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
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-----------------------------------------------------------aaaatgcttgttgctgtttcagaagaccttgctt-tattgcaaggatggtcacttaatcttacttattgggtcttaatatcacatttcttcttacc---tgcagCTTCGCAAACTGTGAGGAAAATTATTGAAATAAATCCGTACATGCTTGGAACAATGGCAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGG
upper sequence: AT1G13060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G102596_T02 (Zea mays), 3'ss of exon 2
gtacaatgaagattaagttagcttgttgttggttttggttttgtgctggagtgtcaaacaaatttctagttttcattctgttggccatta--attgtgaaccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
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----------------------------------------------------------------ctgggttctcttagttaagaaaatcgggactgatgttcatttgtgacatgagattgt-atactgtttcatatgatctcactgttctttttatatttcgcagCCTCACAAACCGTGAGGAAAATTATTGAAATAAATCCTTACATGCTGGGGACAATGGCTGGAGGTGCTGCTGATTGCCAATTTTGGCATAGGAACCTAGG
upper sequence: AT1G13060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G17960.1 (Glycine max), 3'ss of exon 3
gtacaatgaagattaagttagcttgttgttggttttggttttgtgctggagtgtcaaacaaatttctagttttcattctgttggccattaattgtgaaccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
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-----gtgagtgtttgttaattttaactttaatttcactattct--ttgttcctttggtgaatgctgagtttttatgttacttgttactt-ttatctatttgtgg-------------ttgtct--ttgttcttga-attttgagt--gttggctgtctccagCATCGCAGTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGG
upper sequence: AT1G13060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
------gtacaatgaagattaagttagcttgttgttggttttggtt--ttgtgctggagtgtcaaacaaatttctagttttcattctgttggccattaattgtgaaccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
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gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggca------gagttttttgtttttgtgctaattgctgcaaatta--aaatgatgggttttatctat--ttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
upper sequence: AT1G13060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 3'ss of exon 3
gtacaatgaagattaagttagcttgttgttggttttggttttgtgctggagtgtcaaacaaatttctagttttcattctgttggccattaattgtgaa--ccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
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------------------------------------------------------------ctcatctgatcaaaactttg--aaccatgaaatagggagatcttttggactttggatgcattgcctatttgttttcattgtctt---ccttccttatttttgcagCATCACAATCTGTGAAGAAAATTATTGAAATTAATCCCTACATGCTTGGCACAATGGCTGGAGGAGCTGCTGATTGCCAGTTTTGGCACAGAAATTTGGG
upper sequence: AT1G13060.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacaatgaagattaagttagcttgttgttggttttggttttgtgctggagtgtcaaacaaatttctagttttcattctgttggccattaat-tgtgaaccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
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-------------------------------------------------------agtgaggtttcccaaggttgcactatt-----taaatgtatggagca-tgaagaaagggtttagttg-gtacatcttgctgacaagtgcattgtttttccatca--cagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
tgttaat putative branch site (score: 3)
atttttgttaatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatgaagattaagttagcttgttgttggttttggttttgtgctggagtgtcaaacaaatttctagttttcattctgttggccattaattgtgaaccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT