Sequence
atgc intronic sequence ATGC exonic sequence...caaggtactcttatcttgtcatttgctctgagaacactagatcattatctccggttgacactgaattttccatgctttgtgttttgtttttgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAACACTGCAAAGTATAAGATAGACTCTGTTGAGTTTGAATCACTTACTTTGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G050193_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 3
caaggtactcttatcttgtcatttgctctgag--aacactagatcattatctccggttgacactgaattttccatgctttgtgttttgtttt---tgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAACACTGCAAAGTATAAGATAGACTCTGTTGAGTTTGAATCACTTACTTTGG
|||| ||||| ||| || || | ||| || | |||| | | | ||| || || | | || | | ||||||||||||||| ||||||||||||||| || || ||||||||||| ||||| | | ||| ||||| ||||| ||| ||||||||||| |||||||| |||
----gtacgcttatgttgaagattacttctggttgacaataaaa-attaatactcttaagttgtagattacttctggttgacgataaaagttgtgtaacctgtagGCTATCTGCAAAACTGCACAGGATATTGCAAATCCAATTATTGCAGAGAATAAAGAAAAATATAAAATAGATTCTATTGAGTTTGAAACACTTACTCTGG
upper sequence: GRMZM2G050193_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g60340.1 (Oryza sativa), 3'ss of exon 3
caaggtactcttatcttgtcatttgctctgagaacactagatcattatctccggttgacactgaattttccatgctttgtgttttgtttttgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAACACTGCAAAGTATAAGATAGACTCTGTTGAGTTTGAATCACTTACTTTGG
| |||| ||||| || || |||||||| | | | ||||| || | |||||||||||||||||| |||||||||| | || || ||||| ||||| |||||| | |||||||| ||||||| | || |||||||| || |||||||||
----------------------gtactcttctgctg-tagattgtt---tctggttgacaataggactaac-----------tttgtgttcaacctgtagGCTATCTGCAGAATTGCACAGGATGTTGCAAATCCAATCATTGCAAAGAACAAAGAGAAGTATAAAATAGACTATATTAAGTTTGAAACATTTACTTTGG
upper sequence: GRMZM2G050193_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g36770.1 (Oryza sativa), 3'ss of exon 4
caaggtactcttatcttgtcat---ttgctctgag------aacactagatcattatctccggttgacactgaattttccatgctttgtgttttgtttttgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAACACTGCAAAGTATAAGATAGACTCTGTTGAGTTTGAATCACTTACTTTGG
|||| ||||||||| | | | | || | | | || | |||| | |||||| | | | || | || ||| | ||||||| |||||||||||||||| |||||| || |||||||| |||| ||||||| | |||||| |||| ||| ||||||||||||||||||| ||||
----gtacccttatcttgctgtagactacaccaagtcaccaagaatgaaatggatctctctgattgacaatagaaactttat---------tgtgcatttatcctgtagGCGATCTGCAGAACTGCACTGGATATTGCAAAGCCAATCATTGAAGAGAACAGGAAGACGTATAAACTAGAATCTATTGAGTTTGAATCACTTACATTGG
upper sequence: GRMZM2G050193_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT2G20990.2 (Arabidopsis thaliana), 3'ss of exon 3
caaggtactcttatcttgtcatttgctctgagaacactagatcattatctccggttgac-actgaattttccatgctttgtgttttgtttttgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAACACTGCAAAGTATAAGATAGACTCTGTTGAGTTTGAATCACTTACTTTGG
| ||| || || | | || ||| | ||| | | | | | || |||||| || || || | | | || ||||||| || || | |||||| || |||| || || || || |||| ||| | | ||||||| ||||| ||||||||||| |||||| |||||||| | |
---gttaca--tacctggactgatgttcttgtgatacttcactttctcttaccttcatttgctaaattttgaat-tttggtctctccaactatccatgtagGCCATATGTAAGACTGCAAAGAATATAGCAAAACCGATCATTGAGGAGCAGATACCAAAGTACAAGATTGACTCTGTTGAATTTGAAACACTTACTCTAGMapped 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|76014351|gb|DT941521.1|DT941521EST: TTGTTATTGGTTACTTCCTCTTCATCTACGTCCAGCCAACTGATGTCAAG GCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAAC
genomic: TTGTTATTGGTTACTTCCTCTTCATCTACGTCCAGCCAACTGATGTCAAGgtgtgtacat ... tgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAAC
EST:
gi|74238718|gb|DT646632.1|DT646632EST: TTGTTATTGGTTACTTCCTCTTCATCTACGTCCAGCCAACTGATGTCAAG GCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAAC
genomic: TTGTTATTGGTTACTTCCTCTTCATCTACGTCCAGCCAACTGATGTCAAGgtgtgtacat ... tgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctccggttgacactgaattttccatgctttgtgttttgtttttgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAACACTGCAAAGTATAAGATAGACTCTGTTGAGTTTGAATCACTTACTTTGG
ggttgac putative branch site (score: 4)
ttttgtttttgcctt putative PPT
ttttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaggtactcttatcttgtcatttgctctgagaacactagatcattatctccggttgacactgaattttccatgctttgtgttttgtttttgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAACACTGCAAAGTATAAGATAGACTCTGTTGAGTTTGAATCACTTACTTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - -catttgc
- - - - - - - - - - - - - - - - aacacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccatgc