Sequence
atgc intronic sequence ATGC exonic sequencegtataaaaaatctcaccaattcctcaacatgaaatgctccgatcgaatttgctttcgtctcgtgatcgatttgatgatcagATGGACAAGGCGACGATCCTCTCCGACGCGGCGAGCTACATCAGGGAGCTGCAAGAGAAGCTCAAGGCGCTAGAGGAGCAGGCTGCTGCCAGGGTCACCG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g46790.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g46790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G355469_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------gtataaaaaatctcaccaattcctcaacatgaaatgctccgatcga--atttgctttcgtctcgtg----atcgatttgat--gatcagATGGACAAGGCGACGATCCTCTCCGACGCGGCGAGCTACATCAGGGAGCTGCAAGAGAAGCTCAAGGCGCTAGAGGAGCAGGCTGCTGCCAGGGTCACCG--
| || || || | || | | || ||| ||| | | || | |||| | | ||| ||||||||||||||||| |||||||| || |||||| |||| ||| | ||||| || ||||| ||| ||||||||| || || ||| || || ||||
gtcctggactcctggtccaatttactaactgaatcgatcccctgcattcttcttcttcttcttctaccgcatg-catctgttatatattgcgttctgttcctgacgagaagaaaactgcggcgcgtgcaaaacgcgctcgatcggatcagATGGACAAGGCCACGATCCTTTCTGACGCGACGAGATACGTGAGGGATCTCCAAGAAAAGATCAAGGCGCATGAAGA--CGGCGGCGGCAGTAACGACCGGG
upper sequence: LOC_Os03g46790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G137380_T01 (Zea mays), 3'ss of exon 1
--------------------gtataaaaaatctcaccaattcctcaac---atgaaatgctccgatcgaatttgctttcg-----------------tctcgtgatcgatttgatg--atcagATGGACAAGGCGACGATCCTCTCCGACGCGGCGAGCTACATCAGGGAGCTGCAAGAGAAGCTCAAGGCGCTAGAGGA-GCAGGCTGCTGCCAGGGTCACCG--------------------------------------------
| || | | | |||| || || || || || | || | || | | | || | | | | || ||||||||||||||| || ||||| || |||||| |||| || | | |||||| ||||| |||||||||||||| || || | ||| | || ||||
gtgttgatccaatcaatttatcactgaatccccctgcgattcttctaccgcatctgttgttctgttctgttctgttcctgacgaaaagaaaactgcaccgcgcgtgcaacgcgctgggatcagatggacaagggtacaatcctttctgacgcgacgagataagtgaagGAGCTCCAAGAAAAGCTCAAGGCGCTTGAAGACGGCGGCAGTGGCAGTAACGACCGGAGCATCGAATCCTGGGTGCTCATCAAGAAGCCGTGCATCGTAG
upper sequence: LOC_Os03g46790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G036554_T02 (Zea mays), 3'ss of exon 1
-------------------------gtataaa---aaatctcacc---aattcctcaaca-tgaaatgctccgatcgaatttgctttcgtct-cgtgatcgatttgatgatcagATGGACAAGGCGACGATCCTCTCCGACGCGGCGAGCTACATCAGGGAGCTGCAAGAGAAGCTCAAGGCGCTAGAGGAGCAGGCTGCTGCCAGGGTCACCG
||| || || | || | ||| || | ||| ||||| ||| | | || | ||||| | ||| |||||||||||||||||||||||||||||||| || | ||| | | |||||| || || ||||||||| || || ||| || || ||| | | |
gtcctttctcagtcccagccgatccatatgaactgaacccctgcccttgttctctctgcactctgctgcatcgatcaaatccccgataacctgctcgatcg-tggcatgg-cagATGGACAAGGCGACGATCCTCTCCGACGCAGCCAAGTACGTGAAGGAGCTCCAGCAGCGGCTCAAGGCCCTGGAAGAGGCTGCCGCCGCCGCCGCCGGCA
upper sequence: LOC_Os03g46790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G120021_T01 (Zea mays), 3'ss of exon 2
-----------gtataaaaaatctcaccaattcctcaacatgaaatgctccgatcgaatttgctttcgtctcgtgat--cgatt---tgatgatcagATGGACAAGGCGACGATCCTCTCCGACGCGGCGAGCTACATCAGGGAGCTGCAAGAGAAGCTCAAGGCGCTAGAGGAGCAGGCTGCTGCCAGGGTCACCG--
| || ||| ||||| | | | || | ||| | | | ||||| | |||||||||||||||||| |||||||| || |||||| | | || | | || || || | |||||||||| || ||| || ||| || || | | | |
gttctgacccagatcgaatccattcatttgttcctagattatatttctgaagacgaagaccacttaattaatgcaacgacgattaatttctgatcagATGGACAAGGCAACGATCCTTTCAGACGCGACCAAGTATGTGAAAGAACTCCATGGAAAGCTCAAGGACCTGGAG--GCTGGCGGCAGCAACCGGCGCAAGA
upper sequence: LOC_Os03g46790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G155043_T01 (Zea mays), 3'ss of exon 1
----------------------------------gtataaaaaatctcaccaattcc---tcaaca-tga--aatgctccgatcgaatttgcttt----cgtctcgtgatcgatttg--atgatcagATGGACAAGGCGACGATCCTCTCCGACGCGGCGAGCTACATCAGGGAGCTGCAAGAGAAGCTCAAGGCGCTAGAGGAGCAGGCTGCTGCCAGGGTCACCG
| || ||| ||| | || | | ||| | || | | || || | ||| | | | ||||| |||||||||||||||||||||| ||||| |||||| | || ||| | | |||||| ||||||||||| |||| || ||| ||| | | ||| | | |
gtttgatccggatcagattccctgcacctgttcgacaccaataatacatataatcctggatcgatactgatgattgttacaattacatgcatgatgcaacgtataacggttaatttgtgatgatcagATGGACAAGGCGACCATCCTTCTGGACGCGACAAGGTACCTGAAGGAGCTCCAAGAGAAGCTGAAGGATCTGGAGCAGCGGAAGGAGGCCGGCGGCGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgaaatgctccgatcgaatttgctttcgtctcgtgatcgatttgatgatcagATGGACAAGGCGACGATCCTCTCCGACGCGGCGAGCTACATCAGGGAGCTGCAAGAGAAGCTCAAGGCGCTAGAGGAGCAGGCTGCTGCCAGGGTCACCG
atttgat putative branch site (score: 5)
atttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaaaaatctcaccaattcctcaacatgaaatgctccgatcgaatttgctttcgtctcgtgatcgatttgatgatcagATGGACAAGGCGACGATCCTCTCCGACGCGGCGAGCTACATCAGGGAGCTGCAAGAGAAGCTCAAGGCGCTAGAGGAGCAGGCTGCTGCCAGGGTCACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC