Sequence
atgc intronic sequence ATGC exonic sequencegttagtattctatttatttctgtgcttgtgttaccaatttaatgtgaaactgggttaggtcctcatctaattctttgccgcttgctcctgtcttccccatatgcagtagcctgtactacaacgaaaagaacaccatcatgtttgatgatctaagaaggaatttcgtcatgaatccacagAACGGTCTCGTGATCAAGCCATTCAGGAAGAGGCATAATGATCATGAGCTGGTGAAGCTTGCACACTACCTGCTTTCAATCGGAGACCTAGAAGATCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G427526_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 5
gttagtattctatttatttctgtgcttgtgttaccaatttaatgtgaaactgggttaggtcctcatctaattctttgccgcttgctcctgtcttccccatatgcagtagcctgtactacaacgaaaagaacaccatcatgtttgatgatctaagaaggaatttcgtcatgaatccacagAACGGTCTCGTGATCAAGCCATTCAGGAAGAGGCATAATGATCATGAGCTGGTGAAGCTTGCACACTACCTGCTTTCAATCGGAGACCTAGAAGATCTGA
| | || | | || |||||| || | | | ||||| |||| ||||| ||||| |||| | ||||||||||| ||| |||| ||||| |||||||||||||| || |||||||| || ||||||||||||||||| ||||| |||||||| |||| || || || |||
-----------------------gttagtagtggcgtggtactgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctttcatatgcagTA----------CAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT---------------------------------------------------------------
upper sequence: GRMZM2G427526_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G06599.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagtattctatttatttctgtgcttgtgttaccaattta-atgtgaaactgggt-taggtcctcatctaattctttgccgcttgctcctgtcttccccatatgcagtagcctgtactacaacgaaaagaacaccatcatgtttgatgatctaagaaggaatttcgtcatgaatccacagAACGGTCTCGTGATCAAGCCATTCAGGAAGAGGCATAATGATCATGAGCTGGTGAAGCTTGCACACTACCTGCTTTCAATCGGAGACCTAGAAGATCTGA
||||||| | | | || | || || | | |||| || | | | | | || ||||| ||| | | ||||| ||| |||| || ||| ||| ||||| || ||||||||||| ||||| ||||||||||| |||||||| || |||||||| |||||||| || ||||| |
---------gtatttatatat---catgcatcctcatttgacacatgaatcttgatctttttttttatgtaattgattggtgttg--tcctgactt------gtgca-------gTTCTATAACCCTGGTAACACGATAATGTTTGATGACCTAAGGAGGAATTTCGTAATGAATCCTCAAAACGGTCTAACAATCAAGCCGTTTAGGAAAGCTC------------------------------------------------------------------
upper sequence: GRMZM2G427526_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv12s0035g00640.t01 (Vitis vinifera), 3'ss of exon 5
gttagtattctatttatttctgtgcttgtgttaccaatttaatgtgaaactgggttaggtcctcatctaattctttgccgcttgc-tcctgtcttccccatatgcagtagcctgtactacaacgaaaagaacaccatcatgtttgatgatctaagaaggaatttcgtcatgaatccacagAACGGTCTCGTGATCAAGCCATTCAGGAAGAGGCATAATGATCATGAGCTGGTGAAGCTTGCACACTACCTGCTTTCAATCGGAGACCTAGAAGATCTGA
|| || |||| || || | | || | ||| |||| | | | | | | | | | | | | | || ||| | | || ||||| ||| |||||||||||||||||||| || |||| ||||| || ||||| |||||||||||| | |||||||||||||||||| |
-ttcaaatgctatatagaaaattgaat-tattgcatttttcttgtgggcccaa-tgatcttcctacttgacaatagactggtggtatcttgttatttttgca-----------gTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTTGTGATGAACCCACAGAACGGTTTGACAATCAAGCCATTCAGGAAGGCTC------------------------------------------------------------------
upper sequence: GRMZM2G427526_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ35150 (Selaginella moellendorffii), 3'ss of exon 5
gttagtattctatttatttctgtgcttgtgttaccaatttaatgtgaaactgggttaggtcctcatctaattctttgccgcttgctcctgtcttccccatatgcagtagcctgtactacaacgaaaagaacaccatcatgtttgatgatctaagaaggaatttcgtcatgaatccacagAACGGTCTCGTGATCAAGCCATTCAGGAAGAGGCATAATGATCATGAGCTGGTGAAGCTTGCACACTACCTGCTTTCAATCGGAGACCTAGAAGATCTGA
|| | |||| || || |||| || || | | ||| ||| ||| | |||| | | |||| || || | || ||||| |||||||| |||||||| | ||||| ||||| ||||||||||| || |||||||||||| ||| || | || |
-----------------------------gtaaagcgttta----gatccttctttagatc-tcttatcattttttaaattttggtttcttctttctttgctacagTTTTATGGACCA-------AACAACACGATCATGTTGGATGATCTCAAGAGGAACTTCGTGATGAATCCACAAAATGGTCTCGTGATCCGGCCTTTTAAAAAAGCTC------------------------------------------------------------------
upper sequence: GRMZM2G427526_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ24099 (Selaginella moellendorffii), 3'ss of exon 5
gttagtattctatttatttctgtgcttgtgttaccaatttaatgtgaaactgggttaggtcctcatctaattctttgccgcttgctcctgtcttccccatatgcagtagcctgtactacaacgaaaagaacaccatcatgtttgatgatctaagaaggaatttcgtcatgaatccacagAACGGTCTCGTGATCAAGCCATTCAGGAAGAGGCATAATGATCATGAGCTGGTGAAGCTTGCACACTACCTGCTTTCAATCGGAGACCTAGAAGATCTGA
|| | |||| || || |||| || | || || || || | | | | || | || || ||| ||||| |||||| | |||||||| | ||||| ||||| ||||||||||| || |||||||||||| ||| || | || |
-----------------------------gtaaagcgttta----gatccttctttagatctcttatcagtttgtttttttttttcttggtttcttctttctttgcta--cagTTTTATGGACCAAACAACACGATCATGCTGGATGATCTCAAGAGGAACTTCGTGATGAATCCACAAAATGGTCTCGTGATCCGGCCTTTTAAAAAAGCTC------------------------------------------------------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagaacaccatcatgtttgatgatctaagaaggaatttcgtcatgaatccacagAACGGTCTCGTGATCAAGCCATTCAGGAAGAGGCATAATGATCATGAGCTGGTGAAGCTTGCACACTACCTGCTTTCAATCGGAGACCTAGAAGATCTGA
gtttgat putative branch site (score: 5)
aattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtattctatttatttctgtgcttgtgttaccaatttaatgtgaaactgggttaggtcctcatctaattctttgccgcttgctcctgtcttccccatatgcagtagcctgtactacaacgaaaagaacaccatcatgtttgatgatctaagaaggaatttcgtcatgaatccacagAACGGTCTCGTGATCAAGCCATTCAGGAAGAGGCATAATGATCATGAGCTGGTGAAGCTTGCACACTACCTGCTTTCAATCGGAGACCTAGAAGATCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC