Sequence
atgc intronic sequence ATGC exonic sequence...ctctactccataggggtatagagacttcctatgtccagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 4
ctctactccataggggtatagagacttcctatgtccagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
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---------------gtaaaaaggctctatttctattattgactttcgga--tat-tcatgcccttgctctgaccatattat--gttacttgtatggcagGCACACCTTGCTTCCGTGGGTATGGCAGGCGTGATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTCAGCCAGGACCTATCTGTTATTAACTT
upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 4
ctctactccataggggtatagagacttcctatgtc------cagtgtactctcagcaccatcttttactctgattcttatctgaa----cattcgatatcaattc-tgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
| | |||| | || ||| | ||| ||| | ||| || | ||| | | || || | || |||| | | | | || ||| ||||| || |||||||||||||| ||||| |||| ||||| |||||||| ||||| ||||| ||||| || |||| ||||| |||||| |||||||
---------tttgaggtactgtttttttttataactggactcaggaaacttttagc--caacctttgttattttttcaatgttaaatttcatttgttgcttacccatgcagGAACTCCTTGTTTCCGTGGTTATGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT
upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G45770.1 (Glycine max), 3'ss of exon 4
-ctctactccataggggtatagagacttcctatgtccagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
|| | || || || | || | ||| | | || || |||||| | || || | || | | | || ||| ||||| ||||||||||| ||||| |||||||||| ||||| ||||| || ||||| ||||| ||||| || |||| |||||| |||||| | |||||
ttattaatttttaatagtgtaatgcatttgt-tgttatatcaggtgtctacattttcttttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAGCGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 5
ctctactccataggggtatagagacttcctatgtc--cagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatat------caattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
|| || || | | || | | | | || | ||| |||| || | | | || || | || ||| | | | | | ||| ||||| || ||||||||||| || ||||| |||| ||||| |||||||| ||||| ||||| ||||| || |||| ||||| |||||| |||||||
--------agtaaggtcatgtatatttgttttttaggtactgctttttcataaccaatttatgttattggtccaatgttaaatttctgtttgttgcttacctgagcagGAACTCCTTGTTTCCGTGGTTACGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT
upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
----ctctactccataggggtatagag-acttcctatgtccagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
| | | || | | | | || | | || |||| |||| | || ||| | || || | || | | | || ||| ||||| ||||||||||| ||||| |||||||||| || || ||||| || ||||| ||||| ||||| || |||| |||||| |||||| | |||||
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgt-ctct----gctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT
upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------ctctactccataggggtata----gagactt---cctatgtccagtgtactc--tcagcaccatcttttactc---tgattcttatctgaac--attcga-------tatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
| || | | || || || | | || ||| | || ||| | | | ||| | | | ||| ||| ||| || ||| | | || |||||| || ||||||||||| ||||| || ||||||| ||||| |||||||| |||| ||||| ||||| || ||||| ||||| || ||| | |||||
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT
upper sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 4
------------------ctctactccataggggtatag-agacttcctatgtccagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattct-gtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
|||| ||| || | | | | || || || || | | | | | | || ||| |||| ||| | || ||| | ||| || || ||||||||||| ||||| || ||||||| ||||| |||||||| |||| ||||| ||||| || ||||||||||| |||||| | |||||
gtgagtaaactgggactgttctaatccttaaaaactgatcacaacccttaagttca---tattttta-tgcaagttgggtctatgagatttatt---acactttatgcttatttgagcagGTACCCCATGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGGTGCATTGTCAGCCAAGACCTCTCTGTTTTGAACTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
ctctgat putative branch site (score: 4)
atatcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctactccataggggtatagagacttcctatgtccagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGTTGAGCGCAGGAGGAATTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
- ctactcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaaca