Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatcatatttttcattcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggtatatgtattgcttagGTTGATGGTGAATTTGCCGGATGCATCAAATAGAAGAAAAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g22420.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G482077_T01 (Zea mays), 3'ss of exon 2
gtgagtatcatatttttcattcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggtatatgtattgctt-agGTTGATGGTGAATTTGCCGGATGCATCAAATAGAAGAAAAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTA
||||| | || | || | || | | | || || | || || ||| | ||| ||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| || |||||||| || |||||| ||||||| || || ||||| ||| || ||
---------------------------gtgatttatcgtttgtttatagcctaatacaacatctgtcaatggttttttgacctcagtcttatggggcaataatttctttagGTTGATGGTTAATTTGCCAGATGCATCAAATAGGAGAAAAATTCTTAGTGTAATACTAGCCAAGGAAGATATGGCAGACGACGTTGATCTAGAAACTATA
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G370521_T01 (Zea mays), 3'ss of exon 2
gtgagtatcatatttttcattcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggtatatgtattgctt-agGTTGATGGTGAATTTGCCGGATGCATCAAATAGAAGAAAAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTA
||||| | || | || | || | | | || || | || || ||| | ||| ||| ||||||||||| |||||||| ||||||||||| || |||||||||||||| || |||||||| || |||||| ||||||| || || ||||| ||| || ||
---------------------------gtgatttatcgtttgtttatagcctaatacagcatctgtcaatggttttttgacctcagtcttatggggcaataatttctttagGTTGATGGTTAATTTGCCAGATGCATCAAACAGGAGAAAAATTCTTAGTGTAATACTAGCCAAGGAAGATATGGCAGACGACGTTGATCTAGAAACTATA
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G417650_T01 (Zea mays), 3'ss of exon 2
gtgagtatcatatttttcattcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggtatatgtattgctt-agGTTGATGGTGAATTTGCCGGATGCATCAAATAGAAGAAAAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTA
||||| | || | || | || | | | || || | || || ||| | ||| ||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| || |||||||| || |||||| ||||||| || || ||||| ||| || |
---------------------------gtgatttatcgtttgtttatagcctaatacagcatctgtcaatggttttttgacctcagtcttatggggcaataatttctttagGTTGATGGTTAATTTGCCAGATGCATCAAATAGGAGAAAAATTCTTAGTGTAATACTAGCCAAGGAAGATATGGCAGACGACGTTGATCTAGAAACTATG
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 2
gtgagtatcatatttttcattcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggtatatgtattgctt-agGTTGATGGTGAATTTGCCGGATGCATCAAATAGAAGAAAAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTA
||||| | || | || | || | | | || || | || || ||| | ||| ||| ||||||||||| ||||||| |||||||||||||| |||||||||||||| || |||||||| || |||||| ||||||| || || ||||| ||| || ||
---------------------------gtgatttatcgtttgtttatagcctaatacaacatctgtcaatggttttttgacctcagtcttatggggcaataatttctttagGTTGATGGTTAATTTGCTAGATGCATCAAATAGGAGAAAAATTCTTAGTGTAATACTAGCCAAGGAAGATATGGCAGACGACGTTGATCTAGAAACTATA
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 19
gtgagtatcatatttttcattcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggtatatgtattgcttagGTTGATGGTGAATTTGCCGGATGCATCAAATAGAAGAAAAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTA
|||| |||| | | | ||||| | || | | ||| || | ||||| | || ||| | ||| || ||||||||||||||||||||| |||||||||||||| ||||| |||||||| || |||||||| || |||||||||||||| ||||| ||||| |||||| ||
--------------------gtgatttattgtttgt-ttatagc-ctaatacgac-atctgtcaatagttta-ttgacc-----tcagtcttg---tgtgtgttctctagGTTGATGGTGAATTTGCCAGATGCATCAAATAGGAGAAAGATTCTTAGTGTAATACTAGCCAAGGAAGATTTGGCAGACGATGTTGATCTAGAAGCTATA
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 3
gtgagtatcatatttttcattcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggtata-tgtattgcttagGTTGATGGTGAATTTGCCGGATGCATCAAATAGAAGAAAAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTA
||||| | || | || | || | | | || || | || || ||| | || || |||||||||||||||||||||| |||||||||||||| |||||||||||||| || |||||||| || |||||||||||||| || || ||||| ||| || ||
---------------------------gtgatttatcgtttgtttatagcctaatacaacatctgtcaatggttttttgacctcagtcttatggggcaatgatttctttagGTTGATGGTGAATTTGCCAGATGCATCAAATAGGAGAAAAATTCTTAGTGTAATACTAGCCAAGGAAGATTTGGCAGACGACGTTGATCTAGAAACTATA
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 20
gtgagtatcatatttttcattcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggt-atatgtattgcttagGTTGATGGTGAATTTGCCGGATGCATCAAATAGAAGAAAAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTA
|| | | ||| ||| | |||| | |||| || ||| | || | || || | ||| |||| | | | ||||| ||| |||||||| |||||||| ||||| |||||||| |||||||| | || || || |||| ||||||||||||||| |||||| ||| ||||||| ||
---------gtaaactcgttatgttt---gatgttaacttct---tttatttcgtgttttacaaatgagatctatgctaattcgtgttctttgttgaaaaatattg--tagATTGATGGTTAATTTGCCAGATGCTCCAAATAGAGGAAAAATTGTCAGAGTTATTTTAGCAAAAGAAGATTTGGCACCTGATGTTGATTTTGAAGCAATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttttagataattgacttgactatgcatgtgttttggtatatgtattgcttagGTTGATGGTGAATTTGCCGGATGCATCAAATAGAAGAAAAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTA
ttagataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatcatatttttcattcattttaagatttgaactgtggtgctaattttatgatttttagataattgacttgactatgcatgtgttttggtatatgtattgcttagGTTGATGGTGAATTTGCCGGATGCATCAAATAGAAGAAAAATTCTTAGCGTGATACTAGCTAAAGAAGATTTGGCAGATGATGTCGATCTTGAAGCTGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG