Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G13760.2 (Glycine max), 3'ss of exon 4
---------gtatgcttaacccat-ctcatcagactgcgcataaccaaatatgcat-atgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
||| || | | ||||| | || | | || | || ||| || || || || | || | |||||||||||||| || || ||||| ||||||||||| | ||||| || || |||||||| ||||| || ||||||||||| |||||||| |||||||| ||
cttattctgttatcatttatttttattcatctcttgtcttgtattcttgttcatattgtacttcccaagttcattttttactgcattctttctg--cctcagATGAAAAGATAGCCTTGCTGGGTGCCATACAGTCTCTCTTTGAAGGTTCAATGTACACCTTTGTGTTTCTATGGACTCCTGCATTGAGCCCAAATGATGA
upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 4
---------gt-atgcttaacccatctcatcagactgcgcataaccaaatatgcat-atgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
|| || || | ||||| | || | | || | || ||| | || | || |||| ||||||||||||| || || || ||||| || |||||||| | ||||| || || |||||||| ||||| || || |||||||| |||||||| |||||||| ||
tcttattctgtgatcttttattttattcatctcttgtcttgtattcttgttcatattgtacttcccaagttcattgtttactacattc--tttgtgcttcagATGAAAAAATAGCCTTGCTGGGTGCTATACAGTCTCTCTTTGAAGGTTCAATGTACACCTTTGTGTTTCTGTGGACTCCTGCATTGAGCCCAAATGATGA
upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcttaacccatctcatcagactgcg-cataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatct--tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
|| | | | | | | | | |||| |||||| | || || | || |||| | || ||| || |||||||| ||||| |||||||| || || || ||||| ||||||| || ||||||||||| ||||| || || |||||||| || ||||| ||||| |||||
gtgaatctcttaccttaccttggtttttgacatactgtaatatgtctttgcttccagctttattcttccactaaccacctttttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA
upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgcct-----tctaacgctgtccat--ttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
| | || || | || | | | | || || || || || ||||| | |||||| | || || || | |||||||||||||||||||| ||||| || || ||||| | || || | ||| |||||||| ||||| ||||| ||||| ||||| | || ||||| || ||
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA
upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
--gtatgcttaacccatctcatcagactg----cgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtc-catttgatct---tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
||| | | ||| | || | || | | | | | | | ||| || ||| ||| ||| || | |||||||| || || ||||| ||||| || |||||||| | ||||| || || |||||||||||||| ||||| |||||||| || |||||||| ||||||||
atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattt-tctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 4
----gtatgcttaacccat---ctcatcagactgcg-cataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatt-tgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
|| |||| || || | ||| ||| | | | | | | | | ||| | || | | || | | | || ||||||||| || ||||| || ||||| || || ||||| |||||||| ||||| ||||| || ||||| ||||| |||||||| || | || |||||||||||
cattgtttgctatcccaatgggtttatccatctgtttcctcatcttttcagttttttcctcctttcttggagctttagtattatgtttcatgtggttcagATGAGAAAATTGCGTTGCTGGGTGCAATTCAGTCGTTGTTTGAAGGCTCAATGTATACTTTTGTGTTCCTCTGGACTCCTGCTCTAAGCCCAAATGAAGA
upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgt-ttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
|| |||| | | ||| | | || | | || | || | | || || | | |||| | | || ||||||| ||||| || | |||| ||||| ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || || || |
gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtac--tgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtc-actgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------------gtatgcttaa----cccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccat-ttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
|||||| | | || || | | || | || || || | || | | || ||| || ||| | | |||||||||||||||| | |||| || || || || ||||| || || |||||||| |||||||| ||||| ||||| |||||||||||||| |||| |
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttact--tgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA
upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ21113 (Selaginella moellendorffii), 3'ss of exon 4
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
| || ||| | || || | | | |||| ||||| | ||||||||||||||| | || ||||| || || || | || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || || |
-------------------gtaagcttttcatgtctttatgcaagcgagagccttatctttggattcta-----------------tgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA
upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 4
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
| | | | ||| | | | | | | ||||| | || | ||| || | ||||||||||||||| | || ||||| || || || | || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || || |
----------------------------gta-agcttttcatgtctttaatgcaagcgagagccttat----ctttggattctatgt--agATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
tccattt CT-rich tract
atatgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA