Sequence
atgc intronic sequence ATGC exonic sequence...aacattgttgtacagtaacatgtgtgaattttttcccttctgttagaacaaccaattagtattgcagaatgttacactaactacaattcttcctttttagGGCCAAATGTTAACCCTTGTGGAGTACCTTCTGCTTCTTTATCGTGCTTTGTTGCCAACTTCTGTTTGGTATCGTTTCTTTCTGAACAAGGAATATGGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G061980_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 3'ss of exon 4
aacattgttgtacagtaacatgtgtgaattttttcccttctgttagaacaaccaattagtattgcagaatgttacactaactacaa---ttcttcctttttagGGCCAAATGTTAACCCTTGTGGAGTACCTTCTGCTTCTTTATCGTGCTTTGTTGCCAACTTCTGTTTGGTATCGTTTCTTTCTGAACAAGGAATATGGGA
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tatcttgaattctagct-tatttcttattttagatccttttatagttgcaagc--ttagtagttggttctgacttctgaggctcaaactttctgttttgctagGGTCAAATGCTAACCCTTGTGGAATACCTTCTGCTCCTATATCGTGCCTTGTTGCCAACTCCTGTTTGGTACCGTTTCTTTCTGAACAAGGAATATGGGA
upper sequence: GRMZM2G061980_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 4
aacattgttgtacagtaacatgtgtgaattttttcccttctg---ttagaacaaccaattagtattgcagaatgttacactaactacaattcttcctttttagGGCCAAATGTTAACCCTTGTGGAGTACCTTCTGCTTCTTTATCGTGCTTTGTTGCCAACTTCTGTTTGGTATCGTTTCTTTCTGAACAAGGAATATGGGA
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tctgctatc-ttttgtaacatttcctggagttatgggttcaggatctatatcatctttctcatgtcattacattctgatggtactatcattttt--ttgtcagGGTCAAATGCTGACTTTAGTTGAATACCTCCTCCTGCTTTACCGTGCCTTGTTGCCAACACCAGTTTGGTATCGTTTCTTCCTGAACAAAGAATATGGAA
upper sequence: GRMZM2G061980_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G14590.1 (Glycine max), 3'ss of exon 4
aacattgttgtacagtaacatgtgtgaattttttcccttctgttagaacaaccaatt----agtattgcagaatgttacactaact--acaattctt----cctttttagGGCCAAATGTTAACCCTTGTGGAGTACCTTCTGCTTCTTTATCGTGCTTTGTTGCCAACTTCTGTTTGGTATCGTTTCTTTCTGAACAAGGAATATGGGA
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------gtttta--gtagcttcctttctttttctgacagacaaaatagcatatatttttcaagtatagtttcctcctacaatcatctgatagtatttaacttatttcaagGGTCAAATGTTAACTTTGATTGAGTATACTCTGCTGCTGTATCGTGCTTTGTTGCCAACACCAGTTTGGTACCGATTTTTCTTGAACAAGGATTATGGAA
upper sequence: GRMZM2G061980_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0056g00440.t01 (Vitis vinifera), 3'ss of exon 4
-aacattgttgtacagtaacatgtgtgaattttttcccttctgttagaacaacca--------attagtattgcagaatgttacac--taactaca-attcttcctttttagGGCCAAATGTTAACCCTTGTGGAGTACCTTCTGCTTCTTTATCGTGCTTTGTTGCCAACTTCTGTTTGGTATCGTTTCTTTCTGAACAAGGAATATGGGA
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gtaaggtaatatgaaattatgtgttaaagtagatttatttaggttagtatcatttgcatttatattctttttgtctgccattacacactgactccagacatttattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTGTTGCCAGCACCTGTCTGGTATCGTTTTTTCTTGAACAAAGAATATGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacaaccaattagtattgcagaatgttacactaactacaattcttcctttttagGGCCAAATGTTAACCCTTGTGGAGTACCTTCTGCTTCTTTATCGTGCTTTGTTGCCAACTTCTGTTTGGTATCGTTTCTTTCTGAACAAGGAATATGGGA
cactaac putative branch site (score: 1)
caattcttccttttt putative PPT
aattagtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacattgttgtacagtaacatgtgtgaattttttcccttctgttagaacaaccaattagtattgcagaatgttacactaactacaattcttcctttttagGGCCAAATGTTAACCCTTGTGGAGTACCTTCTGCTTCTTTATCGTGCTTTGTTGCCAACTTCTGTTTGGTATCGTTTCTTTCTGAACAAGGAATATGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - -tgttgta
- - - - - - - - - catgtgt
- - - - - - - - - - - - - - - - - -ccttctg
- - - - - - - - - - - - - - - - - - - - - - - - caaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaca