Sequence
atgc intronic sequence ATGC exonic sequencegtaagattatcaaattatccggctaataattattgtttcagtacgtggacacttgggcgtacggttgctgatgatcgatgatgccggttgcgttttccgtgcatgatttttttttttttttggcttagGTGGTCAGCGATCGCGGCGCGGCTGCCGGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTCCTCCGCATGGGCATA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g37210.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g37210.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G031323_T01 (Zea mays), 3'ss of exon 2
----gtaagattatca-aattatccggctaataattattgtttcagtacgtggacac------ttgggcgtacggttgctgatgatcgatgatgccggttgcgttttccgt--gcatgatttttttttttttttggcttagGTGGTCAGCGATCGCGGCGCGGCTGCCGGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTCCTCCGCATGGGCATA
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gtaagtagtagcatcctagctattctggcttcgcttggcttggctttgtgtagcttcgctgtttttgctctactggactggagtagtagctaggcgcagtacggtttctgatggcgtgattggctactggtggttaattagGTGGTCAGCGATCGCGGCGCGGCTGCCCGGGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTGCTCCGCATGGGCATC
upper sequence: LOC_Os07g37210.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G166337_T01 (Zea mays), 3'ss of exon 3
------------gtaagattatcaaattatccg--gctaataatta---ttgtttcagtacgtggacacttgg-gcgtacggttgctgatgatcgatgat--gccggttgcgttttccgtgcatgatttttttt------tttttttggct-tagGTGGTCAGCGATCGCGGCGCGGCTGCCGGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTCCTCCGCATGGGCATA
| | || || ||| | | | || || | ||| | | | | | | || | | | | | | | | || | | || | | | | | || | ||| || ||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
gtaagcacacacacacacctggcatatcatcgatcgtcgagagctagctctggcctggctagtgtagcttcgctgttttttttctctactactagctagtaggaggatcgcagtcgcagtacgttttctgatgcgcgtgattatattgcctacagGTGGTCAGCGATCGCGGCGCGGCTGCCCGGGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTGCTCCGCATGGGCATC
upper sequence: LOC_Os07g37210.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G06190.1 (Glycine max), 3'ss of exon 3
gtaagattatcaaattatccggctaataattattgtttca-gtacgtggacacttgggcgtacggttgctgatgatcgatgatgccggttgcgttttccgtgcatgatttttttttttttttggcttagGTGGTCAGCGATCGCGGCGCGGCTGCCGGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTCCTCCGCATGGGCATA
| | | | || || | | | | || | || | | | | ||| | | | || | | || | ||| | ||| || | |||||| || | || | |||| | || ||||| ||||||||||||||||||||||| | || || | || | | |||
----------------------cacacacacacacacacacacacatatatatatatatatata-tatcttacaagcta-aatggagttgccattgttctaatttgtatgtttctatttgcaagCACAAATGGTCAATCATAACAGCTCACTTGCCCAATAGAACAGACAATGAGATCAAGAACTACTGGAACACCAATGTCAAGAAAAGATTCATAAGAATGA-----
upper sequence: LOC_Os07g37210.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S389_40V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagattatcaaattatccggctaataattattgtttcagtacgtggacacttgggcgtacggttgctgatgatcgatgatgccggttgcgttttccgtgcatgatttttttttttttttggcttagGTGGTCAGCGATCGCGGCGCGGCTGCCGGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTCCTCCGCATGGGCATA
| | | | || | ||| || | || | || || ||| | || | || ||| |||| | || | || || || | || ||||| || || || | || || |||| || ||||||||||||||||||||||||||||| ||| | ||||| ||| | | ||||| ||
-----------------tttgttt--tgttttgtttttttgtgtttttttgtgtgtgtgtgcgagtgc-gtggagcacagaaa--aattgattttttggaatgtgttgttgttgatt------cgcagATGGTCTGCCATAGCTAGCCATCTTCCTCGCCGCACTGACAACGAGATCAAGAACTACTGGAACACACACTTGAAGAAGCGTCTCATGCAAATGGGAATT
upper sequence: LOC_Os07g37210.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S106_216V6.1 (Physcomitrella patens), 3'ss of exon 2
--gtaagattatcaaattatccggctaataattattgtttcagtacgtggacacttgggcgtacggttgctgatgatcgatgatgccggttgcgttttccgtgcatgattttttttttttt--ttggcttagGTGGTCAGCGATCGCGGCGCGGCTGCCGGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTCCTCCGCATGGGCATA
||| || || | | | | | |||| | | | | | ||| ||| | | || | | ||| |||| || |||| | ||| || ||| |||| |||||||| ||||||| | || || || || ||||||||||| |||||||||||||||||||| | || || | | ||||| ||
gtactgaattttcttcccgtcgcgttgggatgtctcatttctgcagacg-----tcgcgcg-----ttggttacactccacaa----aattgtcagttcctaacagcatttctcgtttcttgattgcattagATGGTCAGCCATCGCGGGCCATCTCCCCCAGCGTACAGACAACGAGATAAAGAACTACTGGAACACGCATTTGAAGAAACGTTTGGCACAGATGGGAATC
upper sequence: LOC_Os07g37210.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagattatcaaattatccggctaataattattgtttcagtacgtggacacttgggcgtacggttgctgatgatcgatgatgccggttgcgttttccgtgcatgatttttttttttttttggcttagGTGGTCAGCGATCGCGGCGCGGCTGCCGGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTCCTCCGCATGGGCATA
| |||| || ||| | || ||| || || || | ||| | | | | | || | | | || ||| ||| | ||| |||||||||||| || || | || || |||| || ||||||||||| || |||||||||||||||||| | | ||||| || || | ||||| ||
-----------------------ttgaaatt-ttacttctttttgta-acagttaggactagttatcttgaataccatttttttaatatatcgctttcttatttatttatttatttatattg---tagGTGGTCAGCCATAGCAAGCCATCTTCCCCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACGCACTTGAGGAAGCGACTGCTGCAAATGGGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcgatgatgccggttgcgttttccgtgcatgatttttttttttttttggcttagGTGGTCAGCGATCGCGGCGCGGCTGCCGGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTCCTCCGCATGGGCATA
tttttttttttttttg CT-rich tract
tgcatgattttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattatcaaattatccggctaataattattgtttcagtacgtggacacttgggcgtacggttgctgatgatcgatgatgccggttgcgttttccgtgcatgatttttttttttttttggcttagGTGGTCAGCGATCGCGGCGCGGCTGCCGGGCCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACATCCGCAAGCGCCTCCTCCGCATGGGCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC