Sequence
atgc intronic sequence ATGC exonic sequence...gcagagacctgtactatgctgattatttgtatatatatggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------------------gca-gagacctgtacta------tgctgattatttgtatatat--atggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
||| | | || || | |||||| ||| | || || | | |||||||||||||||| ||||||||||||| |||||||||||| ||||||||||||||| ||||||||||||| || |||||||||||||| ||||||||||
gtaatttatgattacaagcgtttatttttgcctgcaaagaagcattacaactcttttgatactgcacaatttttctattaaagaagtactgattttttctgtacattaaaactcagGTTATAGACAAGTCCTTTGGTTTTGATAGTGCTGTAGAAGAGGCCCAGCGTGCCATTGATGCAGCTCATGTTGAGGCTTCAAGTGCTGAGAATGGAATAG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G01710.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------------------------gcagagacctgtactatg--ctgattatttgtat-atatatgg-ttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
| | ||| | || |||| | | || || | ||||||| || ||||||||||||||||| |||||||| ||||| || || || ||||| ||||| |||||||||||||| ||| |||| ||||| || |
gtgagcatgcttgaattggacatctgaagccttacaatagaagctactttgctgaaaatataaaaaggatttacttttaaactgtcacctaattaaccatgttgtacctgaatcagGTTATTGATAAGTCATTTGGTTTTGACACTGCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------------------gcagagacctgtactatgct--gattatttgtatatatatggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
|| | || | ||| | |||| | | | | | | ||||||||| ||||| || ||||||||||||||||| || || || || || ||||||||||||||||||||||| |||||| |||| ||| ||||| || |
gtatgcttgttcacaatgtcatatttttgtttctccctggaactctaatcttatcattaaaatatatctgaagtgttagttctctatgaggaaacttcatcatgttcggattgtct---tctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGTATTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 8
-----------------------------------------------------------------------------------gcagagacctgtactatgctgattatttgtatatatatgg-ttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
| | ||| | | | | | | | ||| || ||||||||| ||||||||| ||||||| || |||||||| ||||| || || || || || ||| | |||||||||||||| ||| ||||| |||||||| |
gtaatgatgctttagttgtaaaattgtatatgtgaaaattgttatacttttatgctatcatactccaaaggaaaaaggatttgagattaaagtgtcacctatttaatgtcattctgtatttgaattagGTTATTGACAAGTCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCTGAGAATGGAATTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G21370.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------------------gcagagacctgtactatg--ctgattatttgtat-atatatgg-ttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
| | | || | || |||| | | || || | ||||||| || |||||||| |||||||| |||||||| ||||| || || || ||||| ||||| |||||||||||||| ||| |||| ||||| || |
gtaagcatgcttgaattggacatccgaagccttacaatagaagctactttgatgagaatgtaaaaacaacgatatacttttaaacagtcacctaattaaccatgttgtacctgaatcagGTTATCGATAAGTCATTCGGTTTTGACACTGCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATCG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------------------gcagagacctgtactatgctgattatttgtatatatatggtt-aggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
| | | ||| | | | | | | | ||| || || ||||||| ||||| ||| ||||||| || |||||||| ||||| || || || || || ||| | |||||||||||||| ||| || || |||||||| |
gtaatgatgctttagttgtaaaattgtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaag-tgtcacctatttaatgtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------------------------------------------gcagagacctgtactatgctgattatttgtatatatatggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
||| | | | | |||| | | | | | ||||||||| ||||| || ||||||||||||||||| || || || || || ||||||||||||||||||||||| |||||| |||| ||| ||||| || |
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttcatgttcggattgcct---tctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------------------gcagagacctgtactatgctga--ttatttgta-tatatatggt-taggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
| | | ||| | || | || ||| | || | ||||| || |||||||| ||||| ||||||||||| || || || || || ||||| ||||||||||| ||||| ||||| | |||| ||||| || || |
gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgatgatagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------gcaga-gacctgtact----atgctgattatttg-----------tatatatatggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
||| || ||||| | ||| || | ||| | | ||| || |||| |||||||| || ||||| ||||| |||||||||||||| || || || || ||||||||||| ||||||||||| ||| || ||||| || |
gtatgtatctctttctactgctttgtctctatagaagagctgtatttcttatgtggagaaattgagaacttgacttttgtatttgtgcagGTGATAGACAAATCTTTTGGGTTTGACACTGCTGTAGAAGAGGCTCAACGAGCTATTAATGCAGCACATGTGGAAGCCGAGAGTATAGAGAATGGTATCG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 8
------------------------------------------------------------------------------------------------------------gcagagacctgtactatgctgattatt-----tgtatatatatggt-taggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
| | || | | | ||||| || | ||| |||| ||||||| |||||||| ||||| ||||| |||||||| || || ||||| ||||| ||||||||||| ||||| ||| || |||| || ||| | || |
gtacatctctttgtttccttaattgctgattataggaccggttggatattacacctgatttattgcatagatataaattcaaaaacaatttttttcctattttttattgaccaattctctttttagttgatttttacctccgactattgctggtacagGTTATTGACAAGTCCTTTGGCTTTGACACTGCTGTTGAGGAGGCCCAACGTGCTATTAATGCAGCACATGTTGAATCTGAAAGTATCGAGAATTGTATTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------------------------------gcagagacctgtactatgc--tgattat---ttgtatatatatggtt-aggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
||| |||||| | || | | | || | || || ||||||| ||||| || |||||||||||||||||||| |||||||| ||||||||||||||||| || ||||| ||| || |||| ||| ||||| || |
gtacttcttgcctattgcacctgaattaattttgttcttttctccatctttttcaataaaccttgcattagcctgtaatgtgtcttcaccttagactgccttctcttgattcagGTTATTGACAAATCGTTTGGTTTTGATACTGCTGTTGAAGAAGCACAGCGTGCCATTAATGCGGCACATGTTGAATCTGAAAGTATTGAGAATGGTATTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------------gcagagacctgtact---atgctgatt-atttgtatatatatggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
| ||| | | ||| ||||| || | ||||||||||||| || ||||| |||||||| ||||| |||||||| ||||| || || ||||| || |||||||||||| ||| | | ||||| || |
gtaggtttctgacaaatccttgagtctgatattcgtgcaactctcgaaagaatcgaattgtatgatcaagtcttaattgggaccagactttgtgaggaaagacgaattgatttgacctggaattggcagGTTATAGACAAATCGTTTGGGTTTGATACAGCTGTTGAAGAAGCACAGCGCGCAATCAATGCTGCCCATGTGGAAGCTGAGAGTATTCACAATGGCATTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------------------------------------------------------------------------------------------gcagagacctgtactatgctgattatttgta-tatatatggt--taggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
|| || || | | ||| ||| | ||| |||| ||||| |||||||| || |||||||| || || |||||||| |||||||| || ||||||||||||||||||||| |||| | | ||||| | |
gtacgtcactgtcttttgatatacacttggtaggattacgtgcggtagaagtaactaagtttcaggaagctaatatttggatacgtgtgtgcgcaaagactaccagatgacatgattaattatgtattgttttcttgaagtccaagtgtgccaccgtctaatgcatatttgtcgaatgtggtatttgaggtaacagGTCATAGATAAGTCATTCGGATTTGATACAGCAGTGGAAGAAGCTCAGCGTGCAATCAATGCAGCTCATGTGGAAGCTGAGAGTGTTCAGAATGGTCTTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------------------------------------gcagagacctgtactatgctgattatttg-tatatatatggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
||| | || | || || || || | | | ||| |||| |||||||| ||||||||||||||||| || || |||||||| |||||||| |||||||| || || ||||||||| |||| | | ||||| || |
gtacgttttagacacggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagca-acacaagagctgaatggaaaatatggtgcacgtttggc-agGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG------------------------------
upper sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S327_30V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------------------------------gcagagacctgtactatgctgattatttgtatatatatggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
| ||| ||| || | || |||||| | | || || | || || ||||| ||||| ||||| |||||||| |||||||| || || || || |||||||||||||||||||| |||| || | ||||| | |
gtactatacatcatccctactacacagtgacgcgctttttcacatgtgtgcttatttccacatgttgcctgaattcattcgtgtgcgttctgacttgttctcttttggg-atttgtttcaa--tgaacagATAATTGATAAGTCCTTTGGATTTGACACTGCTGTGGAAGAAGCACAACGAGCAATCAATGCAGCTCATGTGGAAGCAGAAAGTACTCATAATGGTGTTG------------------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
ttttgat putative branch site (score: 4)
ttttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcagagacctgtactatgctgattatttgtatatatatggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - acctgta
- - - - - - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaagaag