Sequence
atgc intronic sequence ATGC exonic sequencegtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g15340.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G155816_T01 (Zea mays), 3'ss of exon 2
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacg---attttaaatttaactttatgaatatattgattaacatatatatg-gttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGC---AGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
|| || |||| || | | ||| || | | | ||| | | | | || || || | | | || | |||||||| |||||||||||||||| || || |||| |||||||| ||||||||||||||||||| ||||||||| ||||||||| | |||||||| || ||
------------------------------------------------------------------------------gtaactgactaataacttgaatgcggtgtactagtagaaatctaagagctaataatgtcta-gtgtttcacaatatgtgttcatggtggacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC---
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
| ||| | | | | ||| ||| || || | | ||| || | | || | || | || | | ||||||||| | | ||| | | ||||| || |||||||| | ||| | ||| | |||||||| ||||||||||| ||||||||||| ||||| || || || || || || || || ||
-----------------------------------------------------------atggaaagaaagacatagacttg----ttagccttg-----aaggtta--taatacttcttgagttttttgta-gcatgaactagttaacatatgt--tgatgcttcttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatga-atatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
|| | | | ||||| ||| |||| || | | || | | ||| | || | | || ||| | | || | | ||||||||||| |||| || | ||||||| || ||||||||| | ||| | ||| | |||||||| ||||||||||||||||||||||||||||| || || || || || ||||| || ||
--------------------------------------------------tggaaagaaagacaaaaatatttgtt------------aactatg-----aaggtta--taatgcttcttgagtt---tttgtaacatgaactagttaacatatat-tggt-gcttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G79580.1 (Arabidopsis thaliana), 3'ss of exon 2
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
||| | | || | | || | | | | | | |||| ||| || ||| | |||||| || | | | | | |||| | ||| ||| |||||| || ||| |||| | || | |||||||| ||||| ||||||||||||||||| || ||||| ||||| | || ||||| || || |
------------------------------------------------------------------tgtgtgt-ttaaatatatatatatatatacttaagactataattaacaattgtat------tttttcaattatatttataacaaattttgttgttgtgtgtatgtagAGAAATGCAGAATCGGGTCGGGTCCTCAAAACGAGTGGTATTTCTTTAGCCACAAGGACAAGAAATATCCGACTGGGACCCGAACGAACCGGGCGACAGC
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0085g01210.t01 (Vitis vinifera), 3'ss of exon 1
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttca-caaaatcac--ctaacgatttta-aatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
| | || | ||| | ||| || | | | | || | | || ||| | || || | || |||||| |||||||| |||| | ||||| | || | ||| | |||||||| ||||||||||||||||| ||||| ||||| || || || | || ||||| || || |
-------------------------------------------------------------------------acta-atcagtccgcaatacccaaaagcaagattaaagttgatattattgcagtacggtattgggaaatttttcatgtttttggatttggttg---gcatgcagATAAATGCCGAATTGGATCAGGCTCTCAGAACGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATACCCAACTGGAACTCGAACAAACCGAGCAACCAT
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
----gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgctta-----atttttttcacaaaatcacctaac----gattttaaatttaactttatg---aatatattgattaacatata-tatggttgcattgatgcagATCGATGCAGGATTGGGA---------CGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
| || | || || | | || | | ||| ||||||| || || ||| | || || | || ||| ||| | | | | | || |||| | | ||| | || | | ||| || | || | || |||| |||||||||||| | | | || | || |||||||||||||||||||| ||||| |||||||| |||| | | | |||||
gtaagaatcgatcagaatcctcggtgtactatgta-tgacaccagactagaaaac--acgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcat-cagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatg-cagATCGATGCAGGATTGGG---------ACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT-
| | ||| | | || | | | | || | | || ||| || || | | | | ||| ||| ||| ||| |||| | || | || ||| |||| ||| ||||||||| ||| || | | ||| || ||||||||||||||||||||||| ||||| || || |||| | | || || ||||| |
---------------------------------------------------gcatgaacatgctcatttgaaggacatatttgagtttcgaatttctcccacatagagtttttgttttgggattggtggatatcttgatactgat-gatattca-atttttgtggcgatgtcaggggtatgcagGATCGGGGACGTCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
------gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatg-cagATCGATGCAGGATTGG-GACG--------GGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
| ||| || || |||| | || | || | | || || | | ||||| | | | ||| | ||| | | | | | || || | | | | | | | || |||| | || | | |||| || |||| ||||| ||||| |||| | | ||| || ||||||||||||||||||||||||||||| || || || || | | | |||||
gtaagccaacgaacccacat-tttgcaggat--ttcattaacgttggttgagg---ttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S223_12V6.2 (Physcomitrella patens), 3'ss of exon 2
gtataaacacatatgcttgctaattaattaactagcacttct----ttagaaaatg--aacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcat--tgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGG---------TACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
|||| | ||| | || | | || | ||||| || | || ||| || | | || | | | | || || | || | || |||| ||| | | |||| ||| || | | || ||| || || || || || |||||| |||| || | | | | | ||| || ||||| ||||| | |||||||||||||||||||||||| | | |||||||
gtatgca-acaattcatttcagagtattcg--tagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaag----aactggattgaaaaccacaccacctgatgtgatatttgactccat-acttcatcacctaaaattcgggtg-ttaaatcatgcaacagATCTTTGCAAAATCCAGGCCGACTCAAATGAGAAGCAAACCGATTACTACTTTTTCAGTCGCAAGGACAAGAAGTACCCGACGGGCAACCGCGCCAACCG---------
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatg-tatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatata-----tggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAG---------GAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
||| | | | | | | | | | |||| ||| | | ||||| |||| | | | ||| ||| ||| || | || | | ||| | || | | | ||| | ||||| | | | || | | | |||||| ||| |||| |||||||| ||| | || | ||| || ||||||||||||||||||||||| |||||||| || || || | | |||||||
gtaagcatcggaatcctgaaggtagtatggtgca-gtgttcaacctcctcatctagt--ttcgtcaaaaaataaacatttaaaacagtactatccattgaattg-tgatcaacataag-ctcaagagcatgttctcctcatctatt-gatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgat-cagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
|| || | || ||| ||| || | | | |||| | || | || || || | || | || ||| | ||| || | |||| | | | || || | | | || ||| | | ||||||||||| ||||| ||||||||||||||||| || || | | |||||||
--------------------------------------------gcaagatcatcacact--caagtgccaacctgaagcacgtgcatgtacattgt----aatccaaggaagagtattgggcattgctaactgatagcgtccattg-cagAGGTATGCAAGATTCCAGGC-GACCATTCCGTGAAC------------CAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
|| | | || | | ||| | | || | || || | || || | || || ||||| | || | | || | || | | |||| | |||| || ||| | ||||| | | || |||| | ||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||| | ||||| |
--------------------------------------------gtaagacggtcatccct-caagcttct-catttcggaaaaaaaaaaccgttctttggaagtc--tttgcg-ttctaaatgt--ctcttctctcactgccatcgatgaat-tgcgtttgc-cacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatat-tgattaacatatatatggttg--cattgat----gcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
| ||| | | || | ||||| | | | | ||| | | | ||| | | ||| ||||| || | ||| || | | | || || |||||||| ||||| ||||||||||||||||| || ||||| || | |||||| | ||||| |
-------------------------------------------------------------------------------------------------------gtagtctagtctcctccatttcga---tatgattgcacaccactgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
|| | | || | | | | || | | | | || || || | | || || ||||| | || | | || | || | | |||| | |||| || ||| | ||||| | | || |||| | ||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||| | ||||| |
--------------------------------------------gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaag---tctttgcg-ttctaaatgt--ctcttctctcactgccatcgatgaat-tgcgtttgc-cacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttg--cattgat----gcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
| ||| | | || || | || | | | | | ||| | | | ||| | | ||| ||||| || | ||| || | | | || || |||||||| ||||| ||||||||||||||||| || ||||| || | |||||| | ||||| |
-------------------------------------------------------------------------------------------------------gtagtctagtctcctccatttcgacatgatta-cacacc-actgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
ttaactttatgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT