Sequence
atgc intronic sequence ATGC exonic sequence...cactgaaaacaagcaagtccctgacatgcatatatgcatattacttgttgttgttgttgtttttttttttttgcagactgacactgcctccgtcctacagGAGACTATTGGCTACATTAGATTCCTCCTGAGTCAAATCGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G083749_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g13000.1 (Oryza sativa), 3'ss of exon 4
-------------------------cactgaaaacaagcaagtccctgacatgcatatatgcatattacttgttgttgttgttgtttttttttttttgcagactgacactgcctccgtcctacagGAGACTATTGGCTACATTAGATTCCTCCTGAGTCAAATCGAG
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gcttttgagctgcatgcagcagcttctttcactttataggagtcgtgtgagtgaaagtaaagcaagtctctgacat-gtatacgtgttccttcttttgcagACTGACACTGCATCCGTACTGCAAGAGACCATTGGTTACATTAGATTCCTCCTGGGTCAAATTGAG
upper sequence: GRMZM2G083749_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------------------------------cactgaaaacaagcaagtccctgacatgcatatatgca-tattacttgttgttgttgttgttttttt--ttttttgcagactgacactgcctccgtcctacagGAGACTATTGGCTACATTAGATTCCTCCTGAGTCAAATCGAG
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gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG
upper sequence: GRMZM2G083749_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G20100.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------cactgaaaacaagcaagtccctgacatgcatatatgc-atattacttgttgtt--gttgttgtttttttttttttgcagactgacactgcctccgtcctacagGAGACTATTGGCTACATTAGATTCCTCCTGAGTCAAATCGAG
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gtataattactgattagttccctttactaatcacttgtttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggttgattgatcccttttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgttgttgttgtttttttttttttgcagactgacactgcctccgtcctacagGAGACTATTGGCTACATTAGATTCCTCCTGAGTCAAATCGAG
gactgac putative branch site (score: 2)
cctccgtcct putative PPT
ttgttgttgttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cactgaaaacaagcaagtccctgacatgcatatatgcatattacttgttgttgttgttgtttttttttttttgcagactgacactgcctccgtcctacagGAGACTATTGGCTACATTAGATTCCTCCTGAGTCAAATCGAG
cactgaa
- - - - -caagcaa
- - - - - - - - - - - -acatgca
- - - - - - - - - - - - -atgcata
- - - - - - - - - - - - - - - - - - - - ttacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcctc