Sequence
atgc intronic sequence ATGC exonic sequencegtcagccccttggccctgacttgtacaacctttatttccaaatatgccactaattatgtctgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G067985_T08 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g01600.2 (Oryza sativa), 3'ss of exon 2
-------------------gtcagccccttggccctgacttgtacaacctttatttccaaatatgccacta-attatgtct-gtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
| | | | | || |||| | | | | | ||||| || || |||| | | || | ||||||||||| |||||||| |||||||||||||| || |||||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||||||||||
gtctgattttctttttcttttttactcttacgtaatgtaatgtatgtcgtctcctgctgaatattacattacattacatttcatcatgtagGCTGGTTTCGCTGGGGATGATGCACCAAGGGCCGTGTTCCCTAGTATTGTTGGCCGTCCTCGCCACACCGGTGTTATGGTAGGAATGGGGCAGAAGGATG
upper sequence: GRMZM2G067985_T08 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 2
-----------------------gtca-gccccttggccctgacttgtacaacctttatttccaaatatgccacta--attatgtctgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
|| | | | || | | || || || |||| | | || ||| | |||| || |||||||| || ||||| || ||||| || || || || ||||||||||| ||||| || |||||||| ||||| |||||||| || |||||||
gttagtactttgcagtttcttctgttatgtgtaattgcatctattagtctcggtttcgttatcaaacgatttatttctataatgatctgtgtacagGCAGGATTTGCTGGTGATGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGCCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATG
upper sequence: GRMZM2G067985_T08 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 2
-----------------gtcagccccttggccctgacttgtacaacctttatttccaaatatgccactaattatgtc--tgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
| | | || | | | ||| || | || | || | | |||| | | | |||| || |||||||| |||||||| || ||||| || || || || ||||||||||| ||||| || |||||||| ||||| |||||||| || |||||||
gttagtacttcgtggatttttgttttgttgcatgtgcatatgcaagtcttgagttcataagtga-ataatttattttaatatggaacagGCAGGATTTGCTGGTGACGATGCTCCTAGGGCTGTCTTTCCCAGTATTGTTGGCCGACCTCGACATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATG
upper sequence: GRMZM2G067985_T08 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 2
----------------------------------------------gtcagccccttggccctg-acttgtacaacctttatttccaaatatgccactaat---tatgtctgtcc-------tttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
|| | || | ||| |||| | || ||| ||||||| | | || ||| | | || | ||||||||||||| || || ||||| || ||||| || ||||| |||||| |||| | || ||||| |||||||| ||||| |||||||| ||||||||||
gttagaagatgttttgccaattgatgagtgtttcttgtgccattgaagaagactgttcactctgtgcttgcttagtattcattgttaaatatgatattgatatatatatttttctcgatgtttgcagGCTGGTTTTGCAGGTGATGATGCTCCTAGGGCCGTGTTCCCCAGCATTATTGGGAGACCACGCCATACTGGTGTAATGGTTGGGATGGGTCAGAAGGATG
upper sequence: GRMZM2G067985_T08 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 1
---------------gtcagccccttggccc-tg-acttgtacaacctttatttccaaatatgccactaa--ttatgtctgtccttt-----agGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
| | ||| | || ||||| || | || | | ||| | | || | | | | ||||||| |||||||| || ||||| || ||||| || || || || ||||||||||| ||||| ||||||||||| ||||| |||||||| || |||||||
gttagtacttagcggctttgttttttgtttcatgtgcttgtgcatctgctagccttgagttcataactgaatctttgattttaatatggaacagGCTGGATTTGCTGGTGATGATGCTCCCAGGGCTGTCTTTCCCAGTATTGTTGGCCGACCTCGACACACTGGTGTTATGGTTGGGATGGGTCAAAAGGATG
upper sequence: GRMZM2G067985_T08 (Zea mays), 3'ss of exon 1
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------gtcagcccct---tggccctgac-ttgtacaacctttatttccaaatatgccactaattatgtctgtccttta---gGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
| || || ||| || || || | | || | || | | | || || | ||| ||| ||||||||||||||| || ||||| || || || || ||||| || |||||||| |||||| | ||||||||||||||||| || ||||| ||||| ||||
gtgagttagactgtttatttagatactgtatggttctaaccttctttgttgtacatgtgtaagactactgatcatgatttttgtatattaacagGCTGGTTTTGCTGGTGATGATGCCCCGAGAGCAGTGTTCCCAAGTATTGTTGGTCGTCCTAGGCACACTGGTGTCATGGTTGGTATGGGTCAGAAAGATG
upper sequence: GRMZM2G067985_T08 (Zea mays), 3'ss of exon 1
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------gtcagccc---cttggccctgacttgtacaacctttatttccaaatat-gccactaattatgtctgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
|| | | | | | | | | ||| ||| || | || | || | | ||| | ||||||| |||||||| || ||||| || ||||| || ||||| || ||||||||||| ||||| ||||| ||||||||||| |||||||| || |||||||
attaaactgattctgtttgctgtggcgaggtgaatttgcattcagtgattatctttgttagttttgttttcacacattaacgctgctcaaaaatgtgc---agGCTGGATTTGCTGGTGATGATGCTCCGAGGGCTGTGTTCCCCAGTATTGTTGGCCGACCTCGACACACAGGTGTCATGGTTGGGATGGGCCAAAAGGATG
upper sequence: GRMZM2G067985_T08 (Zea mays), 3'ss of exon 1
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
-------------------------gtcagccccttggccctgact--tgtacaacctttatttccaaatatgccactaattatgtctgtcc---tttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
| ||| | | | |||| | || | | | | | || || ||||| || |||||||||| ||||| |||||||| || | || |||||||| ||||||||||| || || | |||||||| || ||||| || |||||||||||||| |
ctcttttgcatctttatttataatgggcagacattggatgtagactaatttatgatcaatcctctcgaaactgtgtttaattttggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG
upper sequence: GRMZM2G067985_T08 (Zea mays), 3'ss of exon 1
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------gtcagccccttggccctgactt--gtacaacctttatttccaaatatgccactaattatgtctgtcc---tttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
| | | | |||||| || | | | || | ||||| || |||||||||| ||||| |||||||| || | || |||||||| ||||||||||| || || | |||||||| || ||||| || |||||||||||||| |
caattcatgctataatggcgttcatgataatactattcaagtgacttcagttgtgctgtccagaacgaaaccgtgtttaattgtggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACGMapped 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|31355571|gb|CD439928.1|CD439928EST: GTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAG GCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
genomic: GTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagcccct ... tgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
EST:
gi|211380786|gb|FK990764.1|FK990764EST: GTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG GCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
genomic: GTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagcccct ... tgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgacttgtacaacctttatttccaaatatgccactaattatgtctgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
cactaat putative branch site (score: 2)
tctgtccttt putative PPT
tttatttccaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagccccttggccctgacttgtacaacctttatttccaaatatgccactaattatgtctgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG