Sequence
atgc intronic sequence ATGC exonic sequence...caatttacattcacttatgtattgattgtttgctaagtgtgtgcacttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGCACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------------------------------------------------------caatttacattcacttatgtattgattgtttgctaagtgtg-----tgcacttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
||||| | | | | | | | | || ||| | || | | ||||||||||||||||||||||||| | ||||||||||| || || || || || || |||||||||||||| |||||||| || ||||||||||||||||| |
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC-----------------
upper sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
---------------------------------------------------------caatttacattcacttatgtattgattgtttgctaagtgt-----gtgcacttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
||||| | | | | | | | | || ||| | | | | ||||||||||||| ||||||||||| | ||||||||||| || || || || || || |||||||||||||| |||||||| || ||||||||||||||||| |
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC-----------------
upper sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
----------------------------------------------------------------------------------------------caatttacattca-cttatgtattg---attgtt-tgctaagtgt-----gtgcacttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
||| ||| | | | | ||||| | |||| | ||| | | | || ||||||||||||||||||||||||| | |||||||| || || || || || || || |||||||||||||| |||||||| ||||||||||||||||| || |
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC-----------------
upper sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------------------------------------------------------caatttacattca-cttatgtattg------attgtttgcta--agtgtgtgca------cttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
||| ||| | | | | ||||| |||| | ||| | | | | || || ||||||||||||||||||||||||| | |||||||| || || || || || || || ||||||||||||||||||||||| ||||||||||||||||| || |
gttgggttgcattaaaattttgaaaaattcaatattattttgttatttataactttgcttgtactctatctttctaattgtctcccaaaaatataggggtactgattctcatctagcctgtttattgtgaaatgttgtattctattaatttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCATTTGCTGAGAGGAGGGAGTTTGACAAAATTC-----------------
upper sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 12
--------------------------------------------caatttacattcacttatgtattgat--tgtttgctaagtgtgtgcacttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
|| ||| | || | || | | ||| | | ||| | |||| | | | | |||| ||||| ||||| || ||| ||||||||| || || || || || || || ||||||||||| ||||||||||| |||||||| ||||||||||| |
ttactgccattttttatttccttcaagggaattcaatgtcttttcagtttgc-tttatttttattttgctgatctttatgagagacatgca-tataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC-----------------
upper sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 11
-------------------------------------caatttacattcacttatgtattgattgt-ttgctaagtgtgtg---cac---ttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
|| ||| | || || | | ||| | | || ||| | || || | | ||| |||| ||||| ||||| |||||| ||||||||| || || || || || || || |||||||| || ||||||||||| |||||||| ||||||||||| |
ccttttttatttccttggagggaattaaatgtctgttcagtttgctttattttttattttgctgatctttttaatcttatgagacatgcatataatgcagACAGTGGATAATGACCTTGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTGGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC-----------------
upper sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 12
-----------------------------------------------------------------------------------------------------------------------------------caatttacattc-acttatgtattgattgtttgctaagtgtgtgca---ctt-----ttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
|||| || | | ||| || ||| | | | | | ||| | |||||||| ||||| ||||| |||||| ||||||| || || || ||||| || || || ||||||||||| || ||||| || |||||||| ||||| ||||| |
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaatccaaattccttttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC-----------------
upper sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------------caatttacat-tcacttatgtattgatt--gtttgcta-agtgtgtgcactttt--atgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
|| || | | || | |||| | || || |||| | | | ||| || |||||||||| ||||| ||||| || ||||||||||| || ||||| || || || ||||| ||||| || ||||| || | |||||||||||||| |||
gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT-----------------
upper sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
---------------------caatttacattcacttatgtattg---attgtttgctaagtgtgtgcacttttatgt---agactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
||| | | | | || | | || || || | | | || ||| ||| |||||||||| |||||||| || |||||||||||||| || ||| |||| || || |||||||| || || ||||| ||||| |||||||||||||| ||||
gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtgttgtgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC-----------------
upper sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
-------------------------------------------caatttacattcacttatgtattgattgtttgctaagtgtgtgcacttttat-gtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
|||| || | | | ||| | || ||| || || |||||| ||||| ||||| ||||||||||||||||| || || |||||||| || || ||||||||||| ||||||||||| ||||||||||| || || || |
acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC----------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGCACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
tgaaaatatacataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatttacattcacttatgtattgattgtttgctaagtgtgtgcacttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGCACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - -cattcac
- - - - - - - -tatgtat
- - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgcac