Sequence
atgc intronic sequence ATGC exonic sequencegtaagcactaagcaccagcaacggcaacgccatccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g53130.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
------------------gtaagcactaagcaccagcaacggcaacg--ccatccgtt-----tcaacgacgacgatgt--gcttacgt-----tttggttcgtg------tgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
|| || | || || | || || |||| | || | ||| | ||| | ||| | | ||| | || |||| | | |||||||||||||||||||||||||||| |||||||| || ||||| ||||||||||||| |||||||| |||||||||||||||||||||||||||||||
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgcgcgcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G878558_T01 (Zea mays), 3'ss of exon 3
------------------gtaagcactaagcaccagcaacggcaacgccatccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgt--------gtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
|| | | | | | | | | ||| | || ||||| | | ||||| | | |||| | ||| | |||||||||||||||||||||||||||| ||||||||| || ||||| ||||||||||||| |||||||| ||||||||||||||||| ||||||||||||
gtgagttgccgctccatcgtgtttcccttcccgtggaaccatgcatgtcctcc-tctccacgactgtgtta-gcttaaatacacgcacgtgcgtctgttcctctacgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGATCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCATGGTGTTCGAGCACCCGGCGCAGCCGGGCA
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G33490.1 (Glycine max), 3'ss of exon 3
---gtaagcactaagcaccagc-aacggcaacgccatccgtttcaacga--cgacgatg-tgcttacgtt---ttggttcgtgtgcgtg----tgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
| | |||| | | | | || | | | || | | | || ||| || || | || | |||| |||||||||||||||||||||||| || ||||| || || | ||| ||| |||||| ||||| || | |||| || || || | || || || |
ttttttaatttaaagcccttgttgatttttttgtaatacataaaggaagtccaacaaagctttttgtgttacattaatttgggtatgcaatgatgtgtagGGCATGATGAACAACTGCTGGTATAGAGTGAAAACAAATGTGGGCAAGCCTGCCAAGGGTGAGATTGGCATATTGTTTGAACATCCAGCTCAACCAGGAA
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
--------------gtaagcactaagc-accagcaacggcaacgccatccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
||| | | | | ||| | | || || || | | ||| ||||||| || |||| |||| ||||||||||||||||||||||||||||| || || || ||| |||||||| ||||| || | ||||| || ||||| || || || | |
atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttggga-atgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
---------gtaagcactaagcaccagcaacggcaacgccatccgtttcaacga---cgacgatgtgcttacgtttt--ggttcgtgtgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
| | || || | | ||| | || | |||| || | || || | | || | ||| ||||||||||||||||||||||||||||| ||||| || || ||||||||| |||||||| ||||| || | ||||| || ||||| || || || ||||
tagcaataaactattgcccgtgacttaaaatctaatcaaaatctttactaaagtgcccgactttgagtctattttattaaataagttttgacatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 3
---------gtaagcactaagcaccagcaacggcaacgccatccgtttcaacgacgacga-------tgtgcttacgttttggttcgtgtgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
|| | | || | | || | || | || |||| | | |||||| || |||| ||||||||||||| |||||||||||||| ||||| || || ||||| ||| |||||||| ||||| || | ||||| ||||| || || || || ||||
gcatcctctttatttgttgaatttcatttaatatgtttttaatagtgtaaagtctaatgaacccttttgtgttatctttttgg--aatgcaataatgtgtagGGCATGATGAATAACTGCTGGTTCAGAGTGAAAACAAATGTGTGCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAGCATCCAACCCAACCAGGCA
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
--------gtaagcactaagcaccagcaacggcaacgccatccgttt-caacgacgacgatgt-gcttacgttttggttcgtgtgcgtg----tgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
| || || | | || ||| || | || | | ||| | || | || || | || | ||||||| ||||||||||||||||||||||| || || || || ||||| || |||| ||| ||||| || | || |||||||| || || | || || |
tcatagttgcaaacatgagaggcgtgcgtttatgacgtgattttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
---------gtaagcactaag-caccagcaacg-gcaacgccatcc-gtttcaacgacg--acgatgtgcttacgttttggttcgtgtgcgtgtg-tgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
| | | | | | | | | | ||| | | | | || | ||| || | || ||| | || ||||||| ||||||||||||||||||||| |||||||| || | || | | | | | ||| |||| |||||||||||||| | ||||||||
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtg-gcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
--------------------gtaagcactaagcaccagcaacggcaacgccatccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
| | || | || | | | | | | | | || ||| | || ||| || | | |||| | ||| | ||||| ||||||||||||||||||||| ||||||||| | || | | | | | || ||| |||||| |||||||| ||||| || |
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattc--ttcattacaataat--cgctgttctgaatgtcctcgccgtg-gtgtgc-tacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ14822 (Selaginella moellendorffii), 3'ss of exon 4
gtaagcactaagcaccagcaacggcaacgccatccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgtgt--gcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
|| | | | | | || | || | || || | | || | | | | | || |||||| ||||||||||||||||||||| |||||||| | |||| | | | |||| | | ||||| ||||||||||||||||| ||||| ||
-------------gtgagtggaagtgaattctttggattgatcggtg-----gttctcatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCGTCCCTGCAAGGGGAAGCTCGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGCCA
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcactaagcaccagcaacggcaacgccatccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgtgt--gcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
|| | | | | | || | || || || | | || | | | | | || |||||| ||||||||||||||||||||| |||||||| | | |||| | | | ||||| | | ||||| ||||||||||||||||| ||||||||
-------------gtaagtggcagtggatctttgggattgatcggta-----gttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
tgcttac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcactaagcaccagcaacggcaacgccatccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC