Sequence
atgc intronic sequence ATGC exonic sequencegtaaggctcataatcataaatggacacatatttatcgggaagaactgcactaacctaaaactaaacatgtgctctccccccgcaaaatgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g32680.4 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 5
gtaaggctcataatcataaatggacacatatttatcgggaagaactgcactaacctaaaactaaacatgtgctctccccccgcaaaatgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA
|| | || |||| |||| | |||||||| | || ||||||| || | | ||| | | | |||| || || ||| ||||| ||||| ||||||||||| |||||||| |||||||||||||||||||||||||| || || ||||||||||| ||||||| ||| |||||
gtgtgtcttataaccatatttatcgccatatttacatgtaaaaactgcagtagatgaccttctctctctctctccctctcttcaaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATA
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G408242_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------gtaaggctcataatcataaatggacacatatttatcgggaagaactgcactaacctaaaactaaacatgtgctctccccccgcaaaatgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA
|| | || |||| |||| | |||||||| | || ||||||| || | | ||| | | | |||| || || ||| ||||| ||||| ||||||||||| |||||||| |||||||||||||||||||||||||| || || ||||||||||| ||||||| ||| |||||
gtggaggagagtacagtgcaagcccgacttcttgtattttatataaaaaagatgtgtggtgtgtcttataaccatatttatcgccatatttacatgtaaaaactgcagtagatgaccttctctctctctctccctctcttcaaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATA
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G33140.1 (Glycine max), 3'ss of exon 5
------------------------------------------gtaaggctcataatcataaatggacacatatttatcgggaagaactgcactaacctaaaactaaacatgtgctctccccccgcaaa--------atgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA
|| | || | ||| |||| | | | || | |||| | | | | | | | | || | || ||| || ||||||| ||||| | | |||||||||||| || |||||||||||||||||| | | || || ||| | ||||| | ||||| ||||| |||||
gtaagctgtgttagcttataaatttgtcttattttgcttcatgttaa-cttctgatcgtaaaagtgaataatttgtttctgaagttgtctcatgctattatatttcctttctatgctgaaagcacagtgattttgtatgcagACACTGATGACAAGTATAGATATGAAATCAAGGACATACTTGAAATGGAAATGAAGATTTTAGAAGCGCTTAATTATTACCTGGTTGTATACCATCCATA
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G46170.2 (Glycine max), 3'ss of exon 6
--------------------------------------gtaa-ggctcataatcataaatggacacatatt-tatcgggaagaactgcactaacctaaaactaaacatgtgctctccccccgcaaa---------------atgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA
|| | || | ||| |||| | | | || | || | || || | | | || | || || | ||| ||| || |||||| ||||| | | |||||||||||| || |||||||||||||||||| | | || || ||| | ||||| | ||||| ||||| |||||
gtaagctgttagcttataattttttcttaatttgcttcgtgttgacttttgatcttaaaagtgaataatttgtttccaaatttgtctcatgctattatatttcattatttcctttctatgctgaaagcacagtgattttgaatgcagACAGTGATGACAAGTATAGATATGAAATCAAGGACATACTTGAAATGGAAATGAAGATTTTAGAAGCTCTTAATTATTACCTGGTTGTATACCATCCATA
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0360g00050.t01 (Vitis vinifera), 3'ss of exon 5
------------------gtaaggctcataatcataaatgga----cacatatttatcgggaagaactgcactaacctaa-aactaaacatgtgctctccccccgcaaaatgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA
| | | || | | || || | | | | | |||| ||| |||| | || ||| || || | | ||||| ||||| ||| ||| |||||||| || |||||||||||||||||| || | || || || |||||||||||||||| | ||| || ||
gtaatcacttgttactcagcatgatgttgaactgcggttttagttctccagtcttgtggttgacattttatttaacgtaagaactgagtgcctgacactttccctt----tgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAATGAAGATCTTAGAAGCTCTCAACTATTATTTAGTTGTATTCCATCCTTA
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ10868 (Selaginella moellendorffii), 3'ss of exon 5
gtaaggctcataatcataaatggacacatatttatcgggaagaactgcactaacctaa-aactaaacatgtgctctccccccgcaaaatgtagCTTCTGATGAGAAGTAC---CGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA
|| || | | | | | || | | || || || | | || ||||| || || |||||||| | || | || ||||| || ||||| |||||||||||||||||||||||||| || || || || |||||| | || || ||
---------------------------gtaggtacctcgca----ttctttagttcagcagcttcac-tgactttcacttccttgaaatgcagGGTCAGATGAGAATGGCTTTCGCTACGACATCAAAGACATCCTGGAAATGGAAATGAAGCTCCTGGAGGCGCTAGATTACTACTTAGTTATCTATCATCC---
upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ25939 (Selaginella moellendorffii), 3'ss of exon 5
gtaaggctcataatcataaatggacacatatttatcgggaagaactgcactaacctaaaactaaacatgtgctctccccccgcaaaatgtagCTTCTGATGAGAAGTAC---CGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA
|| | || | | | | | | | || || || | | || ||||| || || |||||||| | || | || ||||| || ||||| |||||||||||||||||||||||||| || || || || |||||| | || || ||
-------------------------------gtacctggcattctttcgttcagc---agcttcac-tgactttcacttccttgaaatgcagGGTCAGATGAGAATGGCTTTCGCTACGACATCAAAGACATCCTGGAAATGGAAATGAAGCTCCTGGAGGCGCTAGATTACTACTTAGTTATCTATCATCC---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|29660228|gb|CB656503.1|CB656503EST: TTTACATAAAAAAGATGTGTG CTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAA
genomic: TTTACATAAAAAAGATGTGTGgtaaggctca ... caaaatgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAA
EST:
gi|88306627|gb|CI671386.1|CI671386EST: GAGCACAGTGCAAGCAAGACTTCTTGTCTTTTACATAAAAAAGATGTGTG CTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATG
genomic: GAGCACAGTGCAAGCAAGACTTCTTGTCTTTTACATAAAAAAGATGTGTGgtaaggctca ... caaaatgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaagaactgcactaacctaaaactaaacatgtgctctccccccgcaaaatgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA
tgctctccccccgc CT-rich tract
taaaactaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggctcataatcataaatggacacatatttatcgggaagaactgcactaacctaaaactaaacatgtgctctccccccgcaaaatgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG