Sequence
atgc intronic sequence ATGC exonic sequencegcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g44900.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 1
gcactcccccactttccccctccccacggcggc-ccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
||| | ||| ||| | | || | | | | | | ||||| | | | | || | ||| ||| ||||||| ||| ||| | | ||||| |||||||||||||| |||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---------------------gtccaggagggcgtcgatgtctttgacagcatctggaataaggcacgcccccagcgccctccctccgtttacccggcccctgccagaacttt-------ttctcgcgatttttgttgattttttttgtt----------tgggg-----gcagGTCTACGACACTGAGAATGCCAACCAGAAGGAGAAGTTCGAGGCGGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G04690.2 (Glycine max), 3'ss of exon 1
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagatttt-gtttttttgtttcgctgctgcggcggtggggcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
| || | || || | | | | |||| | |||| ||| | | | ||||||| || || | | ||| ||| | | |||| |||||||| || ||||| |||||||||||||| || || || ||||||||||||||||| |||||||| ||| ||||||| ||||| || ||||| |
--------------------------------------------------------gtacttcatttgtttctctcactttttttttatttaaaagttttcag-----tttttgttcattgtttttagattttcattgcttcggaacaaaatgacgggtttggtttggggatagGTTTACGACACTGACAATGCTAACCAGAAGGAGAAATTTGAAGCGGACCTCAAGAAGGAGATTAAGAAGCTCCAGAGGTACAGAGACCAAATTAAGACTT
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 1
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttg--tttttttgtttcgctgctgcggcggtggggcttgtac---agGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
|||| | | | | | || |||| | |||| | | | || | ||| | | || | |||| ||||||||||| ||||||||||||||||||||||||||||| ||||| ||||||||||| |||||||||||| |||||||||||||||| ||||| |
-------------------------------------------------------------------------------------------------------gtaggtcctcttctcttcttcgattatttcgaattttctcctgtttttggctcacacatggcgttggtgcgttagGTTTACGACACCGATAATGCGAACCAGAAGGAGAAGTTCGAGGCGGACCTGAAGAAGGAGATTAAGAAGCTGCAGAGGTACAGGGACCAGATTAAGACTT
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 1
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgag-attttgtttttttg----tttcgctgctgcggcggtggggcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
|||| | || || ||| |||| | |||| | ||||| | || | ||| |||| ||||||||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||| |||||||||||| |||||||||||||||| ||||| |
-------------------------------------------------------------------------------------------------------gtaggtcattcttctcttctttgattatttcgattttcttctgttttcgactcacacatggcgttgctgcgttagGTTTACGACACCGATAATGCCAACCAGAAGGAGAAGTTCGAGGCTGACCTGAAGAAGGAGATTAAGAAGCTGCAGAGGTACAGGGACCAGATTAAGACAT
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 1
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
| | | || |||| | || | | | | || |||| | | | | | | | ||| || || || | ||||| || || || || |||| || || ||||| ||||| ||||| ||| | |||||||| |||||||||||||||||||| || |||||||||||||| |
-----------------------------------------------------------tttatgcagtggaatgtgagcagaatgtttgttttcgaagcagaaaagttttttactggacagaggaaaaactcggtttcggacttttttggtgt--------------ttcagGTATATGATACAGACAATGTTAATCAAAAGGAAAAGTTTGAGGCGGACTTGAAGAAGGAAATCAAGAAGCTGCAGCGGTATAGAGACCAGATCAAGACAT
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G18230.2 (Arabidopsis thaliana), 3'ss of exon 2
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
|| | || || | | || |||| | | | | | | | ||| || || || | ||||| || || || || |||| || || ||||| ||||| ||||| ||| | |||||||| |||||||||||||||||||| || |||||||||||||| |
--------------------------------------------------------------------gtgagcagaatgtttgttttcgaagcag------aaaagttttttactggacagaggaaaaactcggtttcggacttttttggtgt--------------ttcagGTATATGATACAGACAATGTTAATCAAAAGGAAAAGTTTGAGGCGGACTTGAAGAAGGAAATCAAGAAGCTGCAGCGGTATAGAGACCAGATCAAGACAT
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 1
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagatt-ttgtttttttgtt--tcgctgctgcggcggtggggcttg-tacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
|| || | || ||| | || |||||| || ||| ||| | || | || | ||||| |||||||| || ||||| || |||||||||||||| ||||| || | ||||||||||||||||| || |||||||| || |||||||||||||| |
-----------------------------------------------------------------------------------------------------------gtaatgcctcgtatctcaaatcttattgtttattggttattcgtttcttaatctcctctctttacttcagGTTTACGACACGGATAATGCCAATCAGAAGGAGAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACAT
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S134_165V6.1 (Physcomitrella patens), 3'ss of exon 2
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggtt--ttggtttgtccctctgagattttgtttttttgttt----cgctgctgcggcg-gtggggcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
|| | || | | | | | | |||||| | |||| | | | ||| | || | | || | | | ||||| |||||||| || |||| || |||||||||||||||||||| || | |||||||| || |||||||| ||||| || | || || || |||| ||
--------------------------------------------------------------------------------ttccttactcacgtcatgggcaggtaatgtggttggttgattttgctgacacatctctccacggttctcaacaatgacgtaacatgtcgaggtatcgcagGTTTACGACACTGAAAATGTTAATCAGAAGGAGAAGTTCGAGGCAGATTTAAAGAAGGAAATTAAGAAGCTACAGCGTTATCGTGATCAAATTAAGATGT
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S101_120V6.1 (Physcomitrella patens), 3'ss of exon 2
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcg-gtggggcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
|| | | | | | | ||| || | | | | | || |||| ||| | | || | | | | || | | | ||||| ||||| || || ||||| || ||||||||||||||||||||||| | ||||| |||||||||||||| ||||| || | || || ||||||| ||
----------------------------------------------------------------------gacattgaattactcagatcatggacaatt----aatatcgtcggtggtttttctggtctttctctccgtagtgctgacgaagaaacacgttgaggtgtcgcagGTGTACGATACTGAAAATGCAAATCAGAAGGAGAAGTTCGAGGCCGATTTAAAGAAAGAGATCAAGAAGCTACAGCGTTATCGTGATCAAATCAAGATGT
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ20408 (Selaginella moellendorffii), 3'ss of exon 1
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtt--tcgctgctgcggcggtggggcttgt-acagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
|| || ||| | | | | || ||| | | | ||| | ||||| || || ||||||||||| || || ||||||||||| |||||||| ||||||||||| ||||||||||| ||||| |||||||||||||| |||||||
-----------------------------------------------------------------------------------------------------------------gtatggaaatctatggcgtcgcctcgccattgatcgatcgagaatttttttttcttctcgcagGTGTATGATACCGAGAATGCAAATCAAAAGGAGAAGTTTGAGGCCGATCTCAAGAAGGAAATCAAGAAGCTACAGCGATACAGGGACCAGATTAAGACGTMapped 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|58658862|gb|CK047542.1|CK047542EST: TCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAG GTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGGCGACCTC
genomic: TCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactccccc ... gcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
attttgtttttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA