Sequence
atgc intronic sequence ATGC exonic sequence...atatcatgtcaagagaaatgtcaaaggtattgtcttctggtttatggtgtttaacaagtctttgtagatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G811797_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g44050.1 (Oryza sativa), 3'ss of exon 3
---------------------------atatcatgtcaagagaaatgtcaa-aggtattgtcttctggtttatggtgtttaac-----aagtctttgtagatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
||| | | | | ||| | | || | | ||||||||| || | ||| | | ||| |||||||||| |||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||| ||||| |||||||| ||||||||||
gatgtgttagatgtacggctgtcatgcatacaaataaattgggaggatcaccatctcttatttgctggtttattttgctgaaccgtgtattttgttgcagATATGGGATACTGCTGGCCAGGAAAGGTTTCAGAGTCTTGGTGTTGCATTCTACCGTGGAGCAGATTGCTGTGTTCTAGTTTATGATGTCAATTCTATGA---------------------------------
upper sequence: GRMZM5G811797_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G12630.3 (Glycine max), 3'ss of exon 3
--------------------------------atatcatgtcaagaga-aatgtcaaaggtattgtcttctggtttatggtgtttaacaagtctttgtagatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
|| | | ||| | ||| | | || | || | || || | | |||| |||| ||||| || ||||| || ||||| || || || ||||| ||||| ||||| || || || ||||||||||| || || |||||||||||||| ||||
ctattctacatctcatatttctatttgtctttttaaagttttaagttacaatagtcgaaattttattttgttattaatttccatgttcttaactttacagATTTGGGATACAGCTGGCCAAGAAAGATTCCAAAGCCTTGGAGTTGCTTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGA---------------------------------
upper sequence: GRMZM5G811797_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G04830.1 (Glycine max), 3'ss of exon 3
--------------------------------atatcatgtcaagaga-aatgtcaaaggtattgtcttctggtttatggtgtttaacaagtctttgtagatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
|| | | | | | ||| | | || | |||| || || | | | |||| |||| ||||| || ||||| || ||||| || || || ||||| ||||| ||||| || || || ||||||||||| || || |||||||||||||| ||||
gtctattctacatctcatatttctatgtctttttaaagttttaggttacaatagttcaaattttattttcttattaattttaatgttcttaactttacagATTTGGGATACAGCTGGCCAAGAAAGATTCCAAAGCCTTGGAGTTGCTTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCAATGA---------------------------------
upper sequence: GRMZM5G811797_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT3G18820.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------------------------------------atatcatgtcaagagaaatgtcaaaggtattgtcttctggtttatggtgtttaacaagtctttgtagatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
|| | | || | | ||| |||| |||| ||| | | || |||| ||||| || ||||| ||||||||||||||||| ||||| || || || ||||| || || ||||| ||||| || || |||||||| ||||| ||||
gttcctactagtgctttattagttagtcactcaatattttttttgaagtaagatgcttgtgctcagctcaacctttcacatttgtgtgaattacctttcttgcttgagctcactcac-ttgttcctgtctttactttgtcaatgtgtttattacagATCTGGGATACAGCTGGACAGGAAAGGTTTCAGAGCCTTGGTGTAGCCTTTTACCGTGGTGCTGATTGCTGTGTTCTTGTATATGATGTCAATTCCATGA---------------------------------
upper sequence: GRMZM5G811797_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT1G49300.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------atatcatgtcaagagaaatgtcaaaggtattgtcttctggtttatggtgtttaacaagtc--------tttgtagatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
| | || |||| || | | | | | | || | || ||| | ||| |||| |||||||| |||||||| |||||||||||||||||||| ||||| || || || || || ||||| ||||| || || |||||||| || || |
gaccataagagtgtcttagattaagaattgatcccaagtactatatatattgctctctttgcttgaccataagagctaaggtcttgctttttttttacagATCTGGGACACAGCTGGTCAAGAAAGGTTTCAGAGTCTTGGTGTTGCGTTTTATCGTGGTGCTGATTGCTGTGTTCTTGTATATGATGTCAACTCCGCAA---------------------------------
upper sequence: GRMZM5G811797_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0063g02420.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------atatcatgtcaagagaaatgtcaa-aggtattgtcttctggtttatggtgtttaacaa-gtctttgtagatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
| | | | | ||| || | | ||| | | || || || || | |||| ||||| || ||||| |||||||| || || ||||| || ||||| |||||||| || || ||||| ||||| || || |||||||||||| ||||
gtaccattaaattctgggtatgtctttctgagtttttacttgggtaacatgctaacactttttgcgctaaaatctagtccacttcctttcgttttggcagATCTGGGATACAGCTGGCCAGGAAAGATTCCAAAGTCTAGGTGTTGCTTTCTACCGTGGTGCTGATTGCTGTGTTCTTGTATATGATGTTAATGTGATGA---------------------------------
upper sequence: GRMZM5G811797_T04 (Zea mays), 3'ss of exon 3
lower sequence: PP1S398_18V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------atatcatgtcaagagaaatgtcaaaggtattgtct--tctggtttatggtgtttaacaagtcttt-----gtagatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
| || || | || ||| || ||| | || | || | || |||| |||||||| ||||| || || |||||||||| || || ||||| || ||||| || ||||||||||||||||| |||||||| |||||| |||||
ttttggcggcgccagtattttcgattttcctcggtatctctaactcgtgaaaccgttgcctcatctcgactaacatacgtagagctttttctgctgacagATTTGGGACACAGCTGGACAAGAGCGGTTTCAGAGCCTCGGTGTTGCCTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGA---------------------------------
upper sequence: GRMZM5G811797_T04 (Zea mays), 3'ss of exon 3
lower sequence: PP1S119_112V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------atatcatg-tcaagagaaatgtcaaaggtattgtcttctggtttatggt--gtttaacaagtctttgt---agatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
| | || | || || | || | || || | | || | | | || || | |||| |||||||| || || || || |||||||||| ||||||||||| || || ||||| ||||| |||||||| || || || ||||| ||| |||||
aagatgaggaggagggtctttggtccagcttttatacttgtgactcattccgcctgttct-tcctcagttctaatattcgcacggcttgttttgctgacagATTTGGGACACAGCCGGACAAGAGCGGTTTCAGAGCCTTGGCGTTGCCTTTTATCGGGGTGCAGACTGTTGTGTTCTTGTTTACGATGTCAATGTTATGA---------------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|149063779|gb|EE157647.2|EE157647EST: ATTTCCTCACCAAGGAGGTGCAGTTCGAGGACAGGCTCTTCACTCTGCAA AGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTAT
genomic: ATTTCCTCACCAAGGAGGTGCAGTTCGAGGACAGGCTCTTCACTCTGCAAgtaagattgg ... aaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtgtttaacaagtctttgtagatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
gtttaac putative branch site (score: 3)
ttaacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatcatgtcaagagaaatgtcaaaggtattgtcttctggtttatggtgtttaacaagtctttgtagatatgggacactgctggtcaggaaaggtttcagAGTCTTGGCGTTGCATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAG
- - catgtca
- - - - - - - - - - - - - - - - -cttctgg
- - - - - - - - - - - - - - - - - - - - - - tggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgctg