Sequence
atgc intronic sequence ATGC exonic sequence...ttaattgggcggatttcatcatatatttattgttgtgatcacgaaatgatatggtcttgatgaaatttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGCGGCGGCGGCGGCGGCGAACGTTCGAATATGATGAGCCACG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g34830.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g34830.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 2
--ttaattgggcggatttcatcatatatttattgttgtgatcacgaaatgatatggtcttgatgaaatttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGC--GGCGGCGGCGGCGGCGAACGTTCGAAT-ATGATGAGCCACG
|| ||| | | | || | | | ||| | | | | | | || || ||| | ||| ||||||| | || || || | ||||| ||||||||||| |||| |||||||||||||||||||| | ||||| | | | | || || | ||| || ||| || ||
ttttgattagaaaaggattagaattgcataagttttgatctttcagtttttttttatttttataaaaatggatctgatttt-gttgtgttatggtgc-acagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCGCACCGAAGATGAATCTTGAAATGATTCATAGTT---
upper sequence: LOC_Os05g34830.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 2
-ttaattgggcggatttcatcatatat-ttattgttgtgatcacgaaatgatatggtcttgatgaaatttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGC--CGAGCGGCGGCGGCGGCGGCGAACGTT--CGAATATGATGAGCCACG
|||| || || | || | | || ||| | | || | || || | |||| | || ||| || ||| || | ||||||| ||||| ||||| ||||| ||||| |||||||||||||| | | ||||||| | | | || || | | ||| | | | | | |||
ggaaattattcgttctttcttatctctattgaagttagggatatgaga-aattgaaaattaaaaaaatgtttgcacatgattgttg-tttctgattatgcagCTGGATGACTGGGTGCTGTGTCGAATTTACAACAAGAAAGGTGCAATTGAGAAGCAGCAACCAGCACCGCCACCACCGAGTGGTGTCCACAAAATTGAAT----
upper sequence: LOC_Os05g34830.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 2
--ttaattgggcggatttcatcatatatttattgttg-tgatcacgaaatgatatggtcttgatgaaatttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGCGGCGGCGGCGGCGGCGAACGTTCGAATATGAT-GAGCCACG--
|||| ||||| || || | | | ||| | | ||||| ||||| || ||||| ||| | | | ||| || || || |||||| ||||||||||| |||||||||| |||||||||||||| | |||||| | || | |||| || | | | ||| || || |
gattaagaacagggatta-ataatgtttcaaagtttggttaggtagaaataatatgtgatttggacaattt--ttttaactgttgtgcttattggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTG-TTGCGGTGGTGGA--TCAGAAAGTGGCCAAGTTATCAG
upper sequence: LOC_Os05g34830.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G24220.1 (Glycine max), 3'ss of exon 2
------ttaattgggcggatttcatcatatatttattgttgtgatcacgaaatgatatggtcttgatgaaatttgatttgatttttggtggtttgtg-ttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGC--CGAGCGGCGGCGGCGGCGGCGAACGTTCGAATATGATGAGCCACG
| || |||| || | || |||| ||| | | ||| | || | |||| ||| || ||||| | || ||| || || |||||||| ||||| ||||| ||||||||||| |||||||||||||| | | || |||| | | | | || | | | ||| ||| ||
ttcgttcttatcttagggatatcggaaattaaaaattg--aagattaaaatatg-tgtgcacatgattg---ctgacttaatttt-gatgatttctgatttttgcagCTGGATGACTGGGTGCTGTGCCGAATTTACAACAAGAAAGGTGCAATTGAAAAGCAACAACTACCACCACCGAGTGGGGTCCGCAAAATTGAATGTTCCG--
upper sequence: LOC_Os05g34830.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 2
-ttaattgggcggatttcatcat-atatttattgttgtgatcacgaaatgatatggtcttgatgaaatttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGCGGCGGCG--GCGGCGGCGAACGTTCGAATATGATGAGCCACG
|||| |||| || | | ||| ||| | ||| | || || || ||| ||||||| | || || || | ||||| ||||||||||| |||| |||||||||||||||||||| | ||||| | | |||| ||| | ||| ||| | ||| |
tgcaattttaattgtttcccaatcaaaattagaattgcataagtcttgttctataatttttataaagaaggatctgatttt-gttgtgttatggtgc-acagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCGCAGCGAAGATGAATGTT--GAGATGGTTCATAGTT
upper sequence: LOC_Os05g34830.3 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S15_200V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------ttaattgggcggatttcatcatatatttattgttgtgat-cacgaaatgat-atggtcttgatgaaa---tttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGCGGCGGCGGCGGCGGCGAACGTTCGAATATGATGAGCCACG-----
| ||| | | | | | | || | || | | | || | || | | | ||| ||| | | || | ||||||||||||||||||||||||||||||| || | || | | | || ||||| | || || || | | || |||
gtatgtcctgcattctcctacctcacaaacattcatgtccgctattacgtattttggtgttttctgaaggactttcgattaacccaactcccctacgttcgatttctcttgtttcgtggaacatccacaactatgttaggacgctccgatctgaacgtaacctacatttggtgatgcagCTAGATGATTGGGTCCTGTGCCGAATTTATGAAAAAACCACCCATGCCCAG----CGAGCTGGAAAGGAACAGGAAAATTCCTGCGT-CGAGGAGGTGTTAGCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgatatggtcttgatgaaatttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGCGGCGGCGGCGGCGGCGAACGTTCGAATATGATGAGCCACG
atgaaatttgatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaattgggcggatttcatcatatatttattgttgtgatcacgaaatgatatggtcttgatgaaatttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGCGGCGGCGGCGGCGGCGAACGTTCGAATATGATGAGCCACG
- - - - - - - - - - - - - - -ttgttgt
- - - - - - - - - - - - - - - - - - - -cacgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgatg