Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccataagcatgaatgtatcattctgctggacaagaaaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccataagcatgaatgtatcattctgctggacaagaaaaaatgtacctatat-cgccagttaatgtatttgtccatttttt--ctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA
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---------------------------------------------------------aaagct----actatcatcatagaagtactatgtcatcatttagaaaatactatgaccagatgtatgagctaatgtatttaccaagttttttaccaactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G01510.1 (Glycine max), 3'ss of exon 2
gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccataagcatgaatgtatcattctgctggacaagaaaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA-
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--------------gtaagtcaatc-ttcttcttcatggggca-tgtatgcttcatct-tctcaccaagtaatattagggataatttttatcaactgtcacgaaagattgaaccc----------------tgattgttgagttttttt---caacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGCTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGT-ACCCGC
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G43840.1 (Glycine max), 3'ss of exon 4
gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccat-aagcatgaatg-tatcattctgctggacaagaaaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA-
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------------------------------------------------------gtcaatcttcttcttaatgaaatgggaataatgtttatcaactgt-cacgaaagaatgaaccatgatt--cagttga-------gttctttttttc-----aacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGT-ACCCGT
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 4
gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccataagcatgaatgtatcattctgctggacaagaaaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA-
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---------------------------------------------------tgcttgtacatgttccttgattctgttgggttcac--ttttaatttgtattatctcttgtagttatgttgagatctgattga---attcacttttacttaat--cagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAGGATGGT-AGCCGT
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 4
gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccataagcatgaatgtatcattctgctggacaagaaaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA-
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----------------------------------------------tatgttcctaggctgtgttgggt--tcacttttaatttgtattatctcttgt-----agagttgtagttatgttgagatctgattga---attcacttttacttaat--cagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGT-AGCCGT
upper sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccataag-catgaatgtatcattctgctggacaagaaaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA
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---------------------------------------------------------aatgttgtggttgagaaaatgtgaacttattgtaa-gatacttttggtagtttct-cttatattggtgttaaactcaaatatgaataacatcgtttgtccagGGCTTCAGGGGAGCATGAATCTTCCAGACGGGTGAAGTCTGAACTTCTGGTTCAGGTTGATGGTGTAAACAACAGTTCTACAGGTGAAGATGGTAGTCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA
agttaat putative branch site (score: 4)
tttgtccattttttct putative PPT
attttttctacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccataagcatgaatgtatcattctgctggacaagaaaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG