Sequence
atgc intronic sequence ATGC exonic sequence...agtactgttttattcgttaatcccaccatcatcatacacgaaatgtatctgttcttatataccctttgtgtttctgaatttgttggttatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g53720.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G171987_T01 (Zea mays), 3'ss of exon 1
agtactgttttattcgttaatcccaccatcatcatacac-gaaatgtatctgttcttata-tacc---ctttgtgtttctgaatttgttggttatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
| || | || ||| || | |||| | | | || || ||| | | | ||| |||| || | |||| | | | | | ||||||||||||||||||||||||||||||||| || || ||||||||||| || |||||||||||| |||||||||||||||||||||| |||||||||||||
---cccattgttcacgaaaattccgattttttcattccctgctatctagagattcagggagcatctgtcttgacgtttgtggaattgtcgatgttttgt--gcagAGATATGTGGCGCTGAAGGTGCAGAAGAGCGCTCAACACTACACAGAAGCAGCCATGGATGAGGTCAAGATCTTGAAGCAGATTGCTGATGGTGATCCTG
upper sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009843_T02 (Zea mays), 3'ss of exon 2
agtactgttttattcgttaatcccaccatcatcatacac-gaaatgtatctgttcttata----taccctttgtgtttctgaatttgttggttatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
| || | || ||| || || | || | | | || || ||| | ||| ||||||| | |||||| | | | || |||||||||||||||||||||||||||||||| || || ||||||||||| || ||||||||||||||||||||||||||| | ||||| |||||||||||||
---tccattattcacgaaaattccggattctttattccctgctatctagagattcagggagcgtctgtcttaacgtttctggaattgttgatgctctgta--cagAGATATGTGGCGCTGAAGGTGCAGAAGAGCGCCCAACACTACACAGAAGCAGCCATGGATGAGATCAAGATCTTGAAGGAAATTGCTGATGGTGATCCTG
upper sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G21320.1 (Glycine max), 3'ss of exon 1
agtactgttttattcgttaatcccaccatcatcatacacgaaatgtatctgttcttatataccctttgtgtttctgaatttgttggt---tatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTG-AAGCAGATTGCCGATGGTGATCCTG
| | || || | | | | | || | || | || || ||||| || || || || | | || |||||||||| ||||| |||| || ||||||||||| ||||||||||| |||||||||||||||||||| || || ||| ||||||||||| || || ||||||
---attaggcgatggtttggcactaaactgggagcattttttgattttcgaattttgttgacttgttttgtttttgttgttttttgtgtgtggagatctgcagAGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACCGAGGCGGCCATGGATGAGATAAAAATTTTGCAAGCAGATTGCGGAGGGAGATCCT-
upper sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G07430.2 (Glycine max), 3'ss of exon 1
---agtactgttttattcgttaatccc-accatcatcatacacgaaatgtatctgttcttatataccctttgtgtttctgaatttgttggttatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
||| || | | | || | | | | |||| | | | ||| | ||| || | ||| | | || |||||||||| ||||| |||| || ||||||||||| ||||||||||| ||||| || ||||||||||| | || ||| |||||||||| || || |||||||
cttgacactaaactaggagcagtttttgattttcgatttttgttgacttgttttgtttgtgt-ttttttttttttttttgtgtgtgtg---tggagatctgcagAGATACGTGGCTTTGAAAGTTCAGAAGAGTGCTCAGCACTACACTGAGGCAGCTATGGATGAGATAACAATTTTGCAGCAGATTGCGGAGGGAGATCCTG
upper sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G22840.1 (Arabidopsis thaliana), 3'ss of exon 1
--agtactgttttattcgttaatcccaccatcatcatacacgaaatgtatctgttcttata--taccctttgtgtttctgaatttgttggttatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
| | || || || | || || | | | | | |||| |||||| || || | | || |||| | || | | || || |||| || || |||| | ||||||||||| ||||||||||| || ||||||||||||||||| ||||| ||||| |||||||| || || ||| | |
attgaattgcattgttg--tgattgaactagctttgt-tagagaatgaggaagttcttgtagttagagaattgaatcttgcctttga-attcatttgtttgtagCGATACGTAGCTTTGAAAATCCAGAAGAGTGCTCAGCACTACACTGAAGCGGCCATGGATGAGATAAAGATATTGAAACAGATTGCAGAAGGCGATGCGG
upper sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G53030.1 (Arabidopsis thaliana), 3'ss of exon 1
agtactgttttattcgttaatcccaccat-catcatacacgaaatgtatctgttcttatataccc-----tttgtgtttctgaatttgttggttatatat-----atgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
|||| | ||| | || | ||| | | | |||||| | | ||| | | ||||| | | ||| ||| || | ||||| | |||||||||||||| |||||||||| |||||||| ||||| || || || || |||||||||||||| | || ||| | |||||||| || || || |||
-gtacgcatctatctctctctctcgccacacgaattgcttgaaatgctttagagattaatttttcgttgctttgtttgtgtgattttcttactcgtatatcgaatgtacagAGATATGTGGCTTTGAAGGTGCAAAAGAGTGCTCAGCATTATACTGAAGCAGCCATGGATGAGATAACAATATTGCAACAGATTGCAGAGGGAGACACTG
upper sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G44850.1 (Arabidopsis thaliana), 3'ss of exon 1
agtactgttttattcgttaatcccaccatcatcatacacgaaat-gtatctgttcttatataccctttgtgtttctgaatttgttggttatatat-atgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
| | || | ||| | | || | ||| || || | || || ||| | |||| ||| | | | || || | ||||| || |||| || ||||||||||| || || || |||||||| || ||||||||||| ||||| ||||| ||||| || || ||||| | |
-ttgacttgttgtagagaaatgctaaaggttgaatctttaggcttagatcagtagttctttagt-ttcatgtgtgaagttttgaaagttcttttttgtgtagCGTTATGTAGCTTTGAAAGTTCAGAAGAGTGCTCAACATTATACAGAGGCAGCAATGGATGAGATAAAGATTTTGAAACAGATAGCTGAAGGTGACTCGG
upper sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ10371 (Selaginella moellendorffii), 3'ss of exon 1
agtactgttttattcgttaatcccaccatcatcatacacgaaatgtatctgttcttatataccctttgtgtt-----tctgaatttgttggttatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
| ||| || || | || | || || | | | || || |||| | || | | |||| | || | | |||| | || | || || ||| | || ||||||||||| |||||||||||||| || ||||| ||||||| || | | || || | | || ||||| |
---atcgttagga-cgaagatttcttgatt-tgattcagtgattttttccctttctataggtagctggttccagtgacttaagtttgattttttccttcttccagAAAAATATAGCACTCAAGATCCAAAAGAGTGCACAACACTACACAGAGGCCGCAATGGACGAGATCACAATTCTCACACAAATCAGCAAAGGAGATCCCG
upper sequence: LOC_Os03g53720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ19677 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------------------------------------------------------------------------agtactgttttattcgttaatccca----ccatcatc--atacacgaaatgtatctgttcttatataccctttgtgtttctga-----atttgttggttatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
|| | | ||| | | | | | | | || || || | | | || || |||| | || ||| |||| | || | | |||| | || | || || ||| | || |||||||||||||||||||||||||| || ||||| ||||||| || | | || || | | || ||||| |
gtgagttttctaggatatttctagcatttcttagtggttttcaataggacgacgatttcttgctttgcttcagtgatttttttctttctagaattttttcaagcataggacgaagatttcttgatttgattcagtgattttttccctttctataggtagctggttccagtgacttcagtttgattttttccttcttccagAAAAATATAGCACTCAAGATCCAAAAGAGTGCACAGCACTACACAGAGGCCGCAATGGACGAGATCACAATTCTCACACAAATCAGCAAAGGAGATCCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctgttcttatataccctttgtgtttctgaatttgttggttatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
ttggttatatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtactgttttattcgttaatcccaccatcatcatacacgaaatgtatctgttcttatataccctttgtgtttctgaatttgttggttatatatatgcagAGATATGTGGCGCTGAAGGTGCAGAAGAGTGCACAGCACTACACAGAGGCGGCCATGGATGAGATCAAGATCTTGAAGCAGATTGCCGATGGTGATCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- tactgtt
- - - - - - - - - - - -caccatc
- - - - - - - - - - - - - - - - catacac
- - - - - - - - - - - - - - - - - - - - - - - - -tgttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgttg