Sequence
atgc intronic sequence ATGC exonic sequencegtacgataacattgtcctcgacacgttgggacaacatgcctgaacgtatgataaattagttttttaatgtatatataaccatttttatatacaaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC
Basic information
species | Oryza sativa |
transcript | LOC_Os08g33150.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g33150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G106558_T02 (Zea mays), 3'ss of exon 2
gtacgata---acattgt---cctcgacacgttgggacaacatgc---ctgaacgtatgataaatta-gttttttaatgtatatataacca------tttttatata-------caaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC
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gtgccatgcatgcattgcatacccccacttctgaaaatgaactgtgttctgtatctatcttagattacatatttgaaggaaaataagcttagttttctttttttttaatgttcttaaaaaatgttagGTGGTCAAAGATTGCGTCGCACATGCCAGGACGAACGGACAACGAGATTAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAGGAAGATGGGGATC
upper sequence: LOC_Os08g33150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G33620.1 (Glycine max), 3'ss of exon 2
gtacgataacattgtcctcgacacgttgggacaacatgcctgaacgtatgataaattagttttttaatgtatat--ataaccatttttatatacaaaacatgt-tagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC
|| || | ||| ||||| | | | | | || | | | | |||| | || ||| | | || | | | | | | || |||||||||||||| |||||| | || || || || || || ||||||||||| ||||||||||| ||||| ||||| ||||||||||||||||| ||
----cctagtatggacct---tttgttggaatcatttttttaataataataattgtgattcctttactaattactgatatcttgtatttttttcctcccttatgcagATGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACTGATAATGAGATCAAGAATCACTGGAACACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATT
upper sequence: LOC_Os08g33150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G41180.1 (Glycine max), 3'ss of exon 2
gtacgataacattgtcctcgacacgttgggacaacatgc--ctgaacgta-tgataaattagtttttta-atgtatatataaccatttttatatacaaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC
| | || | | || | || || | | | || | | |||| || || | || | | | | ||||||| | | | | || |||||||||||||| |||||| | ||||| || || || || ||||| || || || |||||||| ||||| ||||| ||||||||||||||||| ||
--tttttcatgtttttttatgacttttagattaaaattcggttagtcatactcttttattaattattgatatttttttcttgtcatttttttttttac------tcagATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAATCATTGGAACACACACATAAAGAAAAAGCTCAAGAAAATGGGCATT
upper sequence: LOC_Os08g33150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G04580.1 (Glycine max), 3'ss of exon 2
gtacgataacattgtcctcgacacgttgggacaacatgcctgaacgtatgat--aaattagttttttaatgtatatataac---catttttatatacaaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC-
|| | | | || | | | || || | | | ||| | |||||| | || || || | || | | | ||| || |||||||||||||| |||||| | || || || || || || ||||||||||| |||||||| || ||||| ||||| ||||||||||||||||| ||
---------agttatttttcctatgtaaacattcctagtatggaccttttgttggaatcatttttttcctttactaattacagatgtcctttttttccccttatgc-agaTGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACCGATAATGAGATCAAGAATCACTGGAATACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATTG
upper sequence: LOC_Os08g33150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G39530.1 (Glycine max), 3'ss of exon 2
gtacgataacattgtcctcgacacgttggga--caacatgcctgaacgtatgataaattagttttttaatgtatatataaccatttttatatacaaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC
| | | | || | | | || | | ||| | | | | ||| | | | | | || || |||||| | | | | || ||||| |||||||| |||||| | ||||| || || || || ||||| || ||||| |||||||| ||||| ||||| ||||||||||||||||| ||
tttctttcattttcgcgtgttttcttttgtaatcaatactatatactatttaatactactatatatcattttactaattgtcattttcctttttac------tcagATGGTCCAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAACCATTGGAACACCCACATAAAGAAAAAGCTCAAGAAAATGGGCATT
upper sequence: LOC_Os08g33150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G66230.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacgataacattgtcctcgacacgttgggacaacatgcctgaacgtatgataaattagttttttaatgtatatataaccatttttatatacaaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC
|| | | ||||| ||| | || | |||| || ||||| | | | | | ||||| ||| || |||||||| ||||| || |||||||| || || || || |||||||| |||||||| || |||||||||||||||||||||||| | | ||||||||||||
-------------gttaacaa-acgtttcttacttgtgctttaagtttcgatatgttctgtttttgagattt-tgt-----tttttgtatgtaa--------agGTGGTCAAAGATAGCTTCTCATTTACCAGGAAGAACAGACAACGAAATCAAGAATCATTGGAACACTCACATCAAGAAGAAGTTGAGGAAAATGGGGATT
upper sequence: LOC_Os08g33150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0006g00450.t01 (Vitis vinifera), 3'ss of exon 2
gtacgataacattgtcctcgacacgttgggacaacatgcctgaacgtatgataaattagtt-ttttaatgtatatataaccatttttatatacaaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC
| | | |||||| || | | ||| | | | || || | ||||||| ||||| | ||||| | || | || ||||| |||||||| |||||| | || || || || || ||||| ||||||||||| ||||| || ||||||||||| || || || || ||||| ||
-ttccttttttttgtccctgaaat-taattccaaaacatatccatgtgaaattcttcttcaattttaatttatatgt--ttgttttttca-acgtggatttgcagATGGTCCAAGATTGCTTCTCATCTACCAGGAAGAACCGATAACGAAATCAAGAACCATTGGAATACCCACATCAAGAAAAAACTTAAAAAGATGGGTATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataaattagttttttaatgtatatataaccatttttatatacaaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC
atataac putative branch site (score: 3)
attagttttttaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgataacattgtcctcgacacgttgggacaacatgcctgaacgtatgataaattagttttttaatgtatatataaccatttttatatacaaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA