Sequence
atgc intronic sequence ATGC exonic sequenceAGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g52840.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaa-atgtttaatctgaaagagaaatcag------------------------------------------------
|||| ||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||| |||||| | | ||||||||||| | || | |||| ||| ||| || | || || ||| || |
AGAATTTCACGTCGGTGTCAGTGATGCAGGCAGTGGGTTCCGTCATGACCAACAAGTACAGCGAGGGGTACCCTGGCGCAAGATACTACGGGGGAAATGAgtactgcc----ctgctctatcggttgtcattctcgtgattgtttcagtggaaacacgcgtgcaaattgagtgactgtctgggtgaataatctgaattggggtttttattctgtgtgttcttggtcgcag
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G27710.1 (Glycine max), 5'ss of exon 5
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcag--------------------
|||| ||||| || ||||| |||||||| || || ||||| || ||||||||||| ||||| ||||||||||| || || ||||| || |||||||| ||||||| | | || | || | | | |||||| ||| | | ||| | |||| | | ||| ||
AGAATTTCACTTCTGTGTCTGTGATGCAAGCAGTTGGATCTGTGATGACCAACAAATACAGTGAGGGGTACCCTGGTGCAAGATATTATGGTGGAAATGAgtacgtctctctcacttttttcatctacatgtgttcatatt-caggctcctctaaagttactaatttagagagtaaaacatgtaattttagttgatgagaa
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcag-------------------
|||| |||||||| ||||| |||||||| ||||| ||||| || ||||||||||| ||||| ||||||||||| || || ||||| || |||||||| ||||| | | | || | | | | | | |||| | | ||| | | | | | || || ||| ||
AGAATTTCACCTCTGTGTCTGTGATGCAAGCGGTTGGATCGGTTATGACCAACAAATACAGTGAGGGGTACCCTGGTGCAAGATATTATGGTGGAAATGAgtatgtgtctctcactttttgcatctacatgttttcatactcaggctcctttatagttactaacttagagagtaaaacaagtaattttagtttacgagaa
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacgg-----ttgattgcgttctatcggttgcctttgttcagattatt--tgggtgttaaaaat-gtttaatctgaaagagaaatcag---------------------------------------------------------------------------------------------------------------
|||||||||| || |||||||| ||||| || || || || | ||||| |||||||||||||| || || || ||||| |||||||| || ||||| ||||| | || ||| | || | | || |||| | ||| | || | || || || || || || || |
AGAACTTCACTTCTGTGTCAGTTATGCAAGCTGTTGGGTCTATTATGACAAACAAGTACAGCGAAGGATATCCAGGCGCTAGATACTATGGAGGAAATGAgtaagaagatattaatttccttatcatgattttctttcgtggtatttgtaatgtttattggtcatcgtggtatttgtaatgtctattggtcattgttatcatttagcattatcatatttatgtagtcagttccagtgttcattcttttggatttcctggttagtactgaagtagaaagagtgaaaccttttatctttcag
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacgg-----ttgattgcgttctatcggttgcctttgttcagattatt--tgggtgttaaaaat-gtttaatctgaaagagaaatcag---------------------------------------------------------------------------------------------------------------
|||||||||| || |||||||| ||||| || || || || | ||||| |||||||||||||| || || || ||||| |||||||| || ||||| ||||| | || ||| | || | | || |||| | ||| | || | || || || || || || || |
AGAACTTCACTTCTGTGTCAGTTATGCAAGCTGTTGGGTCTATTATGACAAACAAGTACAGCGAAGGATATCCAGGCGCTAGATACTATGGAGGAAATGAgtaagaagatattaatttccttatcatgattttctttcgtggtatttgtaatgtttattggtcatcgtggtatttgtaatgtttattggtcattgttatcatttagcattatcatatttatgtagtcagttccagtgttcattcttttggatttcctggttagtactgaagtagaaagagtgaaaccttttatctttcag
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EDO97448 (Chlamydomonas reinhardtii), 5'ss of exon 5
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcag-----------------------------------------------------
|||||| ||||||||||||||||||||||||||| ||||||||||| | |||||||| || ||||||| | |||| | | || || | | || | | |||| | |||||| | | | |
-------------------------------GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCA-TTGACCAGGCAG-AGCGCCTGTGCCAGgtgggaat-ctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgctgaggggcttgctggtggatcttggacctgcgcgggttc
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S51_296V6.1 (Physcomitrella patens), 5'ss of exon 3
----------------------AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttcta----tcggttgcctttgttcagattatttgggtgttaaaaatg--tttaatctgaaagagaaatcag
|||| ||||| || || ||||| |||||||| || || |||||||||||||| |||||||| || || || || || || || |||||||| ||||| | || | | | |||| | | | ||| |||| || | | | || | |||| |
GGCCTCGAGTTGATCCCATCAGAGAATTTCACGTCTGTTTCAGTTATGCAGGCAGTAGGTTCCGTCATGACCAATAAGTACAGTGAAGGATATCCTGGTgctctctagtacggtggtaacgaatgcgtcttctccccttctcgtctttaatcgattttcttcaacacatcttcactgcgacattggatgtaatttttcc----------
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S21_270V6.1 (Physcomitrella patens), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattat-ttgggtgttaaaaatgtttaatctgaaagagaaatcag-------------------------------------------------
| ||||||||||| | ||||| |||||||| ||||| || |||||||||||||||||||| ||||| |||||||| || | ||||||||||| |||||||| | | | ||| || || || | || | || | | | | ||| || | | | |
AAAACTTCACCTCCCTCTCAGTTATGCAGGCAGTGGGGTCAGTCATGACCAACAAGTACAGTGAGGGTTACCCCGGGGCTCGTTACTACGGTGGCAACGAgtatg-tcaccttttctctgcttcgtggtgttatt-acatgacgttaaacttcattactattt--tccaagtgtagttttggtggtcgtttacgtgtgatcagttgggctgacagcgctacccgtccgcag
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttg---ttcagattatttgggtgtt-----aaaaatgtttaatctgaaagagaaatcag------------------------------------------------
|||| || || || || ||||| |||||||| ||||| || ||||||||||| |||||||| || || |||||||| || | || |||||||| ||||||| || | | || | | |||| | | || | || | | | ||| |||| ||| |||| | |
AGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtttctcattttcctctctctctttaaaatataacttgtctgtattctttttcataaaccttta--ttgattgagatttttgctctgttcatgaatagttaggtatattgacacctctacacaaatgtag
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ16660 (Selaginella moellendorffii), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcag
|||| || || || ||||| ||||| || ||||||||| |||||||||||||||| |||||||| || || || || | |||||||||||||| ||||| ||| | || | | || | | | || || | || |||| |||
AGAATTTTACTTCAACTTCAGTCATGCAAGCAGTGGGATCCATCATGACCAACAAGTATAGCGAGGGCTATCCAGGAGCTCGTTACTACGGTGGAAATGAgta-ggtcgttttttcttcacaagtgacgtcta---ggaacgcttaa-tatt-----tgttcgttctag------------
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ32604 (Selaginella moellendorffii), 5'ss of exon 4
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcag
|||| || || || ||||| ||||| || ||||||||| |||||||||||||||| |||||||| || || || || | |||||||||||||| ||||| ||| | || | | ||| | | | | | || |||| |||| |||
AGAATTTTACTTCAACTTCAGTCATGCAAGCAGTGGGATCCATCATGACCAACAAGTATAGCGAGGGCTATCCAGGAGCTCGTTACTACGGTGGAAATGAgta-ggtcgttttttcttcacaagttacgtctaggaacgcttaatgtttgtt-----tgttcgttctag------------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|58691682|gb|CK080369.1|CK080369EST: AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGA TGCCTGATGGGAGTGAATGATGTGAATTTCTGGTGGCTCTGGGTTTTCCTT
genomic: AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... gagaaatcagTGCCTGATGGGAGTGAATGATGTGAATTTCTGGTGGCTCTGGGTTTTCCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA