Sequence
atgc intronic sequence ATGC exonic sequence...gatgatattgatgttgactagaggttggtgctttccttttggtaccttgattcagtcatggtttcttttgttaaacatatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G029735_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 4
gatgatattgatgttgactagaggttggtgctttccttttggtaccttgattcagtcatggtttcttttgttaaac--atatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGAC-ATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG
|| || || || | || ||| || | || | | | ||| |||||| || | ||||| || || | |||| |||||| | ||||||||||||||||||||||||||||| |||||||||||||| | | || | | ||| | | | | |||
------gttaatatttcct-----tctgtttttttctcatatcctgtttgctaacacgcc-tttattttgtcaagcttatatgtatgtaaaatgttttgcagGTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAA------------
upper sequence: GRMZM2G029735_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 4
gatgatattgatgttgactagaggttggtgctttccttttggtaccttgattcagtcatggtttcttttgttaaac--atatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGAC-ATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG
|| || || || | || ||| || | || | | | ||| |||||| || | ||||| || || | |||| |||||| | ||||||||||||||||||||||||||||| |||||||||||||| | | || | | ||| | | | | |||
------gttaatatttcct-----tctgtttttttctcatatcctgtttgctaacacgcc-tttattttgtcaagcttatatgtatgtaaaatgttttgcagGTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAA------------
upper sequence: GRMZM2G029735_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
gatgatattgatgttgactagaggttggtgctttccttttggtaccttgattcagtcatggtttcttttgttaaacatatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACAT-CACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG
||| | || || || | || | || | || | | | |||| || || | || | | | | | | | | ||||| | || ||| | |||||||| || || ||||||||||||||||| |||| | | || | | ||| || |||
------------gttta-tatagtttcat-ctgctcaaatgattccaagctgtaa----agtttgattatttgattattttcttttt--ggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA------------
upper sequence: GRMZM2G029735_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 4
gatgatattgatgttgactagaggttggtgct-ttccttttggtaccttgattcagtcatggtttcttttgttaaacatatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACAT-CACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG
||| | || | | || | |||||| | || |||| ||| | | | | | | ||||| | || ||| | |||||||| || || ||||||||||||||||| || | | | || | | || || |||
-----------------------gttaatataatttcatctgctcaaatgattccatgctgtaaagttttatta------ttttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA------------
upper sequence: GRMZM2G029735_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
gatgatattgatgttgactagaggttggtgctttccttttggtaccttgattcagtc-atggtttcttttgttaaacatatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG
||||| | | | || | || | | ||| | | | || | | | || | |||||| |||| ||||||||||||||||| || ||||| |||||||| || || | | | | | |||| | | | | ||
---------------------------gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaaacgtttccattatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA----------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgattcagtcatggtttcttttgttaaacatatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG
ccttgat putative branch site (score: 5)
cttttttc putative PPT
ttttgttaaacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgatattgatgttgactagaggttggtgctttccttttggtaccttgattcagtcatggtttcttttgttaaacatatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - tgatgtt
- - - - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - ttttggt
- - - - - - - - - - - - - - - - - - - - - - - -tgattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcata