Sequence
atgc intronic sequence ATGC exonic sequencegtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 6
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagt-tcacaagaaagaagtgcaaatataactctga-actgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
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--------------------------------gtatgttacatctatcatatcatgt--ttgcaacatagttaattaattgtgaaattatggttttaatattgatgtggactacagGAAATCCAAGAGTCACACCAGAGGTTACAAGGGACGTATGCCTGTTAGCTAGAATGATGGCTGCTAACTTATACTATGCACAGATAGAGGATCTGATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 4
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
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------------gtattagtcttatttgtg------attaaaaaaaatagtgtatattatcatagtacactggacatatggaatgatatg----caaattaa-atatggtacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------gtacatagcattctctctcc-----cttatttggatagtatatttgat---------gtgctgaatcatgc-----aactgtagttcacaagaaagaagtgcaaatataactctgaa-----ctgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
| | | | || | | || | || | || |||| | | || || | || | ||| | | || | | | | || || || || || | ||| ||| ||||| ||||| || || || ||||| |||||||| || ||| ||||||||||||||||||||||| |||| | ||||||||||| || |||||
gtatctttcttttggctaagaaattaaagaaacaagcttttttatctaactctttgtgacaattccttactttttgcccccaaatattcatatagactaaatatctttttcagcttcagttttggacaccgcctcagagatgtggcttgtaatatacttattagtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACCAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATGTGTACTTCTCTCAGATAGAAGATCTCATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 4
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
| || || |||||| | |||| | | | || || | | | ||| | || ||| | ||||| || || | ||| |||| ||||||||||| || ||||| || ||||| ||||| ||||| ||||||||||||||||||||||| ||||| | |||||||||| | || |||||
--------actgctacctaggttatttcagttacttattaaaag-gtgtcatgattctattaagcttctcc--gaaagtgtgtgtgtctaactatgt-tcaatatg-atg-cagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 5
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
| || || | ||| | | || | | | | || || | | | ||| | | || ||| ||||| || || | ||| |||| ||||||||||| || || || || || || ||||| ||||| ||||||||||||||||||||||| ||||| | |||||||||| || || |||||
--------actgctagctaggtagtttcagttatttactaaaag-gtatcatgattctgttatgcttctc--ggaaagtgtgtgtgcctaactatgt-tcaatatg-atg-cagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGGATCTTATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G43050.1 (Glycine max), 3'ss of exon 4
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
| | | | || | | || || | ||||||| | | | |||| || | ||| | | || |||| | |||| || || || || || ||||| |||||||||||||| || ||| |||||||||||||||||||||||||||| | ||||| || || || |||||
-----------tgtgccaaaatcccttaaacataatccttcaagtgctgaggtgtt---ttctcgttcctaacagtgaatcaacctctcactatttgtctaatgtgtgttgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------gtacatagcattctctctcc-----cttatttggatagtatatttgat----gtgctgaatcatgc-----aactgtagttcacaagaaagaagtgcaaatataactctgaa-----ctgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
| | | | || | || || | || || ||| | || | || | | ||| | ||| | | || | | | | || || || || || | ||| ||| ||||| ||||| || || || |||||||||||||| || ||| ||||||||||||||||||||||| |||| | |||||||| || || |||||
gtatctttcttttccctaagaaattaatgaaacaagcatttttattaacctctttgttacaattccttactttttgtccccaaatgttcatatgtatatctttttcaacttcagtttgggacactgcctcagagatgtggcttgtaatatacttattggtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 5
gtacatagcattctctctcccttatttggatagtatatttgat-gtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
||| ||| || | | | || ||||| ||| | || || | | ||| || ||| || ||||||| | | || | || | ||||| ||||||||||| || || || || ||||||||||| ||||| |||||||||||||||||||||||||||||| || ||||||||||||| || |||||
gtat-tagtcttatttgtgattttaaaaaatagtgtatattatcgtagtatactggacaaatg----------gaatgatatgcaaattt---tatgttccaatat--gatacagGTAATCCAAGAGTAACTCCTGAAGTGACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAATTTGTATTATTCCCAGATAGAAGATCTTATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
| | |||| ||| ||| ||| | | | || |||| || || |||| | || ||| ||| || |||||| ||| || || |||| || || || |||||||| ||||||||||| || ||||||||||||||||||||| | || ||||||||||||| || |||||
---------gtacactcttgcttctttc----ttat-ctcaaaccattaaaacatg-aattg--gttcttatga-----gtgaaaacatt-ttctgaatc-----------tagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTATTAGCTAGAATGATGGCTGCTAATCTCTACTTCTCCCAGATAGAAGATCTTATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 4
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
|||||| |||| | | | | |||| || || ||| || || || | | || | | || || | ||| | || | | |||| || ||||| || || || || || || || ||||| |||||||| ||||||||||||||||||| | |||| | ||| || ||||| || |||||
gtacat----ttctacaagtccttctcgcatagctctcttattgcgctccctctcttaatggttttactcatgtcacaaactcaca-atatatgtgtatttg---------cagGTAACCCAAGGGTTACACCTGAAGTCACCAGAGATGTTTGCTTGTTAGCTAGAATGATGGCTGCTACTATGTACTTTAACCAAATCGAAGATCTTATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtg-caaatataactctgaactgatgtccatga----cagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
||| || | | | || || | |||| | | | | | | || | || ||| |||| ||||| || ||||| || ||||| || || ||||| |||||||||||||||||||||||||| ||| | || || ||| || || | ||||||||
--------------------------------gtacatgcgtttttttggattactggcaaacgaatcactctcttgttttctcttgttcaccctctaatcgtcgtatctgaatttcagGTAATCCGAGGGTCACACCTGAGGTCACTAGAGATGTGTGCTTGTTGGCTAGAATGATGGCTGCCAATCTCTACTATAACCAAATCGAGAATCTGATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 4
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
| | || | | ||| | || | || | | || | || || | || || | | | | || ||| || |||||| ||| |||| || || || || || || || |||||||||||||||||||| ||||| ||||||||||||||||| |||||| || | |||||||| ||||| |||||
----aaaccaatggaaatt--ttaagtaaatggaatttcttattta--aaacca--cttctaagatt----atgatgtattggtggcttaatgttgctttgatgtggatggcagGAAACCCCAGGGTAACACCTGAAGTTACAAGGGATGTATGCTTATTGGCCAGAATGATGGCTGCTAACTTGTATTATTCTCAGATAGAGGACCTTATGTT
upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 4
gtacatagcattctctctccctt-atttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
| | | || || | | || || |||| | | | | || || | | || || | ||| ||| | |||| || ||||| || || || ||||| ||||||||||| ||||| ||||||||||||||||||||||| || || || |||||||||| || || |||||
--------taatttatcaaagttgagtcagactcattagttgac-taccagttatagaaagcaggactctctctcccctgg-attaacatgcttttgacatgaaat-----gcagGTAACCCAAGGGTGACTCCTGAGGTCACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTATACTATTCCCAGATAGAGGATCTTATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
aactgat putative branch site (score: 3)
aaatataact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT