Sequence
atgc intronic sequence ATGC exonic sequence...tctttgttcatccattttgtggtgtaattgaccttttcctaatatgtgatgccccattccgtatgatggatggcgtaacttgttttcctatttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g52370.1 (Oryza sativa), 3'ss of exon 4
tctttgttcatccattttgtggtgtaattgaccttttcc-taatatgtgatgccccattccgtatgatggatggcgtaacttgtttt------cctatttg----cctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA
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----------agtgtggaattgctcagttgctcttttcgataattcttggtccaactctgtctatg-tatatatcatggcttatttttaacctcttatttctgccctttagGTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAAGTGATA
upper sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 4
tctttgttcatccattttgtggtgtaattgaccttttcc-taatatgtgatgccccattccgtatgatggatggcgtaacttgtttt------cctatttg----cctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA
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----------agtgtggaattgctcagttgctcttttcgataattcttggtccaactctgtctatg-tatatatcatggcttatttttaacctcttatttctgccctttagGTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAA------
upper sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
tctttgttcatccattttgtggtgtaattgaccttttcctaatatgtgatgccccattccgtatgatggatggcgtaacttgttttcctatt------tgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA---
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------tctaagtaagttgtggtatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
upper sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 5
tctttgttcatccattttgtggtgtaattgaccttttcctaatatgtgatgccccattccgtatgatggatg-gcgtaacttgttttcctatt-tgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA---
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--tatgtctaagtaagttgtggtatttttgtcattttaatgtgctttgagggtaaatcatgaaatatatctttatgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
upper sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G35020.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------tctttgttcatccattttgtg-gtgtaattgaccttttcctaat--atgtgatgccccattccgtatgatggatg------------gcgtaacttgttttcctat-------------ttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTA---GCGAAA
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gtgagtagttctcatttcagttctgtctttgctgaacatcttctatacgttcttgcaaatttccttagcaagttcagattctcttgttttagtgaatgcgacattcaataacagatgacgtttactgttgttacctgtatattttgttaccttaccataataattttatcatctcagATATCGGACTGCCATCTGGGAAATCACTTTTTCAGATTCAAGCTGAGAGGATCTTATGTGTCCAAAGGCTTGCTTCTCAGGCAATGAGTGAGG
upper sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
------tctttgttcatccattttgtggtgtaattgaccttttcctaatatgtgatgccccattccgtatgatggatggcgtaacttgttttcctatttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA---
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attcagtccatgtttgttgaatttatagaggtggtttttattttcagataattgttcctcaaattcttctgtttatttgtgtacgcctatttcatgt------cagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG
upper sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 4
-------tctttgttcatccattttgtggtgtaattgaccttttcctaatatgtgatgccccattccgtatgatggatggcgtaacttgttttcctatttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA---
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nnntcagtccatgtttgttgaatttatagaggtggtttttattttcagataattgttcctcaaattcttctgtttatttgtgtacgctatttc-------atgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgatgccccattccgtatgatggatggcgtaacttgttttcctatttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA
gcgtaac putative branch site (score: 3)
ttttcctatttgcctc putative PPT
ttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctttgttcatccattttgtggtgtaattgaccttttcctaatatgtgatgccccattccgtatgatggatggcgtaacttgttttcctatttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - catccat
- - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggatg