Sequence
atgc intronic sequence ATGC exonic sequence...tagatagtataacatatagttaattccaaacctacatgtcaacttcttttgaactcgatcatcaccaactgatacaacattggtgcgtttcattttgtagCTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAATATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G158489_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g09000.1 (Oryza sativa), 3'ss of exon 4
tagatagtataacatatagttaattccaaacctacatgtcaacttcttttgaactcgatcatca-ccaactgatacaacattggtgcgtttcattttgtagCTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAATATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCG
| | | | | | |||| || || || || | | ||| | ||| | || ||| |||| | |||||||||||| ||||| || |||||||| ||||||| |||||| ||||| ||||||||||||||||||||||| | |||| ||||||||||||||||||| ||
-actcttttttagaccgaagcgattctttgaacctttggttttcgtccctgtgctttattgtgaattgacttttgcaatactgctgcttttcctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAATATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCG
upper sequence: GRMZM2G158489_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT3G52190.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------------------------------------------tagatagtataacatatagtta-attccaaacctacatgtcaacttc--ttttgaactcga--tcatcaccaactgatacaacattggtgcgtttcattttgtagCTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAATATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCG
|| | || | || |||| | || | || | || || |||| | ||| | | ||| || | | |||||||| | |||||||||||||||| | ||||||| | ||||||||| || ||||||||||| ||| || || || || | |||| || |
gtaaatactggaatcttctcaaccaccatccccccttttatattatttgtaatgcaaaactgtaattgaggtagtaaaaaatggtcttctgtatagagctgagaattgggttatacaacacaaatagtaattaatggagattgtgaaacgaaacccattgtgtgcatctttctcatatttgtatatttttttgtagTCTTGACTCAGAGTTCTTAGCTACAACATCAACTGATGGATCAGCTAGAATATGGAAAGCAGAAGATGGTTTTCCTTTGTCTACTTTGGAACGTAGTGGG
upper sequence: GRMZM2G158489_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0074g00010.t01 (Vitis vinifera), 3'ss of exon 4
tagatagtataacatatagttaattccaaacctac-atgtcaacttcttttgaactcgatcatc-----accaactgatacaacattggtgcgtttcattttgtagCTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAATATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCG
| | | || | ||||| ||| | || | || || || || | || || || | | | || | | || | ||| | ||| |||||||||||| ||| ||||| | ||||| ||||| ||||||||||||||| |||| || | || || | ||||||||| ||||
------ctttccaaaattggaaattcaaaatagattatctgaatttaaagaaaattctacaatttgatagttaaatgtttagccttctatgtctgtaatgctccagCCTCGACACAGAGTTCTTAGCTTCCACATCTACAGATGGTTCTGCAAGAATATGGAAGATAAATGATGGTGTTCCTTTGACTACTTTGACTCGCAACTCGMapped 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|22490777|gb|BU050700.1|BU050700EST: CTTTTGGATGAGCCCAAAGCTCATAAATCCTTCTGAGACATGGATATCAG CTTAGACTCAGAGTTCTTAGTTTCAATATCCATTGATGGATATGCAAGAAT
genomic: CTTTTGGATGAGCCCAAAGCTCATAAATCCTTCCGAGACATGGATATCAGgtcagaacag ... cattttgtagCTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAAT
EST:
gi|19058827|gb|BM737494.1|BM737494EST: CTTTTGGATGAGCCCAAAGCTCATAAATCCTTCTGAGACATGGATATCAG CTTAGACTCAGAGTTCTTAGTTTCAATATCCATTGATGGATATGCAAGAAT
genomic: CTTTTGGATGAGCCCAAAGCTCATAAATCCTTCCGAGACATGGATATCAGgtcagaacag ... cattttgtagCTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttgaactcgatcatcaccaactgatacaacattggtgcgtttcattttgtagCTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAATATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCG
aactgat putative branch site (score: 3)
tttcatttt putative PPT
tttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagatagtataacatatagttaattccaaacctacatgtcaacttcttttgaactcgatcatcaccaactgatacaacattggtgcgtttcattttgtagCTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAATATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA