Sequence
atgc intronic sequence ATGC exonic sequencegtatgattgagaaaaaaacaaacattcttttagcttcttcactttatcactaacaatgagtgataatgcatattattgggtttattctttattgattgatgaacgtggaattattattattttacagGTTTGATGCAGTGATACATTTTGCTGGACTTAAAGCAGTTGGTGAGAGTGTAGAGAAGCCTTTGCTTTATTATAATAATAATCTTGTTGGTACTATTACT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G10960.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g15420.1 (Oryza sativa), 3'ss of exon 2
gtatgattgagaaaaaaaca--aacattcttttag-cttcttcactttatcactaacaatgagtgataatgcatattattgggtttattctttattgattgatgaacgtggaattattattattttacagGTTTGATGCAGTGATACATTTTGCTGGACTTAAAGCAGTTGGTGAGAGTGTAGAGAAGCCTTTGCTTTATTATAATAATAATCTTGTTGGTACTATTACT
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gtaaaacacgctataaaatagtattatctttttattcctttttacttcttttatacttttcaaaagcagcaatttgtaacatctctgtaaagtaaaagtatctaaattcctaaaatatgtc-ttttctagATTTGATGCTGTCGTTCATTTTGCTGGTCTGAAAGCTGTGGGTGAAAGTGTGCAGAAGCCATTGCTTTATTATGACCATAATGTTGCTGGGACAATAATT
upper sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
gtatgattgagaaaaaaacaaacattcttttagcttcttcactttatcactaa--caatgagtgataatgcatattat-tgggtttattctttattgat--tgatgaacgtggaattattattattttacagGTTTGATGCAGTGATACATTTTGCTGGACTTAAAGCAGTTGGTGAGAGTGTAGAGAAGCCTTTGCTTTATTATAATAATAATCTTGTTGGTACTATTACT
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gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtttagccttgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT
upper sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 2
---------------------gtatgattgagaaaaaaacaaacattcttttagcttcttcactttatcactaacaatgagtgataatgcatattattgggtttattctttattgattgatgaacgtggaattattattattttacagGTTTGATGCAGTGATACATTTTGCTGGACTTAAAGCAGTTGGTGAGAGTGTAGAGAAGCCTTTGCTTTATTATAATAATAATCTTGTTGGTACTATTACT
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gtaaggatttggcagaaatttttataattgaaaaagaaaaaaatgattgtt------cttttctttgtcggtgc---ttcatgttttcttgtactagtttgttaagttgtaactgtttttcattcatgtatgtgtctttttcctgcagGTTTGATGCTGTGATACATTTTGCTGGGCTTAAGGCAGTGGGTGAAAGCGTGGATAAACCACTGCTCTACTTTGACAACAACTTGATAGGGACAATCGTT
upper sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G02690.2 (Glycine max), 3'ss of exon 2
gtatgattgagaaaaaaacaaacattcttttagcttcttcactttatcactaacaatgagtgataatgcatattattgg---gtttattctt----tattgattgatgaac-gtggaattat-tattattttacagGTTTGATGCAGTGATACATTTTGCTGGACTTAAAGCAGTTGGTGAGAGTGTAGAGAAGCCTTTGCTTTATTATAATAATAATCTTGTTGGTACTATTACT
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------gtaaggattaggcagaaattttttataataattgaaaaaacaaagaaaaaagtattgttcttttctttgtcggtgcgtcttgttttcttgtactagtttgtaagttgtaactctgtcttttttcctgcagGTTTGATGCCGTCATACATTTTGCTGGGCTTAAAGCAGTGGGTGAAAGCGTGAAGAAACCACTGCTCTACTTTGACAACAATTTGATAGGGACAATCGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattgggtttattctttattgattgatgaacgtggaattattattattttacagGTTTGATGCAGTGATACATTTTGCTGGACTTAAAGCAGTTGGTGAGAGTGTAGAGAAGCCTTTGCTTTATTATAATAATAATCTTGTTGGTACTATTACT
ttatttt CT-rich tract
tggaattattattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattgagaaaaaaacaaacattcttttagcttcttcactttatcactaacaatgagtgataatgcatattattgggtttattctttattgattgatgaacgtggaattattattattttacagGTTTGATGCAGTGATACATTTTGCTGGACTTAAAGCAGTTGGTGAGAGTGTAGAGAAGCCTTTGCTTTATTATAATAATAATCTTGTTGGTACTATTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC