Sequence
atgc intronic sequence ATGC exonic sequencegtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g01480.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G440219_T01 (Zea mays), 3'ss of exon 1
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
| || || | | | || | | |||| | | | | | ||| || | | | || | | | | | ||| | | ||||| ||| | | || || | | | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| || |||||||
acaaatattcgagaacggagacac-tactgctatat-acattctttcagagtatg-gtatatcacatcctcctacgacacatgcacattattattatta-----gcagACAAGTGCAGACTG---GGAGGCCCTGGTGAGGAGGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACCCGGACCAACCG
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
|| || | | | || | ||| || | | | | || | | | || || | | ||| | | || | | | | | || ||| | | || || || |||||| ||||||||||||||| || || || ||||||||||| || ||||| || | |||||
-----------gtttagcaggaaaat-----cctatcatc--tctctttagtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataat-ttagAGTTATGCAAGATAGGAAACGAAG-AGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------gtcagtac-tcagtacagtacgtaca-tgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagc-cagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
||||| | | | | || | || | | | | || | | || | || | || | || |||| || | | ||| |||| ||| |||| | || | | ||| | || ||||| |||||||||||||||||||| ||||| |||||||| |||| | | | ||
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccga-tgtggtcat-----cagAAGTGTGCAGGATTGGGGACGACCCACC---AGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
----gtcagtactcagt-acagtacgtacatgcatg-catatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCG--------GAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA-------------
| | |||| | || || || || | | || || | | || || | ||| | | || | || ||| || | ||| || | | ||| || |||| | || || || |||| || ||||||||||||||||||||||| ||||| || || |||| | | ||
gcatgaacatgctcatttgaaggacatatttgagtttcgaatttctcccacatagagtttttgttttgggattg-gtggatatc--ttgatactgatgatattca-atttttgtggcgatgtcaggggtatgcagGATCGGGGACGTCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------gtcagtactcagtacagtacg-----tacatgcatgcatatg-atagatgtgtaca-atattcgtgtgctaattaagccagcaataatta-actgggagta-taaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
| |||| | ||| || || || || ||||| ||| || | || | |||| | || ||| || | | || | || ||| | | | ||||| ||| | || | || || | ||| | |||| ||| ||||||||||||||||||||||||||||| || || || || | | | ||
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGA---CGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S223_12V6.2 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------gtcagta--ctcagtac--agtacgtacatgcatgcatatgatagatgtgtacaatattcg-tgtgctaattaagccagcaata-attaact-------gggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
|||| || | | || | || || | | | ||| || ||| | | |||| || || | | | | || | || ||| || || |||||| |||| | |||| ||| | | || || ||| |||| | ||| | ||||| ||||| | |||||||||||||||||||||||| | | ||||
gtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaagaactggattgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgca-acagATCTTTGCAAAATCCAGGCCGACTCAAA---TGAGAAGCAAACCGATTACTACTTTTTCAGTCGCAAGGACAAGAAGTACCCGACGGGCAACCGCGCCAACCG
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------gtcagtactcagtacagtac-gtacatgca--tgcatatgatagatgtgtacaatattcgtgtgctaattaa--gccagcaataattaa-ctgggagtataaccatgcatgcagAGCGTTG-CCGGATCAATGGCGGGTCGGCGGCG--------GAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
| | | | | ||||||| | ||| | || | | | | | | | | | || || | | |||| || | | | ||||| || | || | | || || || |||| | || ||| | || | || ||||||||||||||||||||||| |||||||| || || || | | ||||
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaag----ccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
|| || || || | | ||| | ||| | | || | || ||| | || |||||| || | |||| ||||||| ||| ||| |||| | | | | |||||| | ||||||||||| ||||| ||||||||||||||||| || || | | ||||
-------gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgt--ccat---tgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAAC---CAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
----gtcagtactcagtacag-tacgtacat-gcatgcatatgatagatgtgtacaa-tattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
| | || || | || | | | | | | | | | | | | | || | || | || |||| | | | | | | | || || | ||| | | || | || || | ||| || ||||||| |||| |||||||||||||||||||| |||||||| |||||||| ||||||||||||||
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatg--aattgcgtttgccacaca----cagAACGGTGCCGAATTGGCTCCGC-GGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
||| || || | | | | | |||| | ||| | ||| | || | || | |||| | | || || | |||||||||||| ||||| ||||||||||||||||| || ||||| || | |||||
---------------------------------------------gtagtctagtctcctccatttcgatatgattgcacaccactgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGG-ATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
--------gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaa-tattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
|||| |||| | | | | | | | | | | | | || | || | || |||| | | | | | | | || || | ||| | | || | || || | ||| || ||||||| |||| |||||||||||||||||||| |||||||| |||||||| ||||||||||||||
gtaagacggtcatccctcaa-gcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatg--aattgcgtttgccacaca----cagAACGGTGCCGAATTGGCTCCGC-GGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
||| || || | | | | | | |||| | ||| | ||| | || | || | |||| | | || || | |||||||||||| ||||| ||||||||||||||||| || ||||| || | |||||
---------------------------------------------gtagtctagtctcctccatttcgacatgattacacaccactgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGG-ATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA
aataattaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT