Sequence
atgc intronic sequence ATGC exonic sequence...cttagtcatttaccagcacatatacctttcacgttttaagaataatcacacttggctttggtgctttgtttatataaattgtataattatatgattttagGATGACAAAAAATTTCAAGGTGAGCTCTTTGGGATATGCAATCTGTTTCGCGACTTGTCTGATAAGCTTTTCACCAGTGAGATCATTGAAATGCATGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g15890.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g15890.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G146041_T01 (Zea mays), 3'ss of exon 6
-----cttagtcatttaccagcacatatacctttcacgttttaagaataatcacacttggctttggtgctttgtttatataaattgtataattatatgattttagGATGACAAAAAATTTCAAGGTGAGCTCTTTGGGATATGCAATCTGTTTCGCGACTTGTCTGATAAGCTTTTCACCAGTGAGATCATTGAAATGCATGGAG
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gactgcacaatagtttaattcggattggccttttggtagttgtaagttaacagcttactgactagatatctggtgtccatt--ttggataattct---gatttagGATGACAAGAAATTTCAAGGTGAGCTCTTTGGGATCTGCAATCTTTTCCGTGACTTGTCCGATAAGCTTTTTACTAGTGAGATTATTGAGATGCATGGAG
upper sequence: LOC_Os05g15890.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G146041_T03 (Zea mays), 3'ss of exon 5
-----cttagtcatttaccagcacatatacctttcacgttttaagaataatcacacttggctttggtgctttgtttatataaattgtataattatatgattttagGATGACAAAAAATTTCAAGGTGAGCTCTTTGGGATATGCAATCTGTTTCGCGACTTGTCTGATAAGCTTTTCACCAGTGAGATCATTGAAATGCATGGAG
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gactgcacaatagtttaattcggattggccttttggtagttgtaagttaacagcttactgactagatatctggtgtccatt--ttggataattct---gatttagGATGACAAGAAATTTCAAGGTGAGCTCTTTGGGATCTGCAATCTTTTCCGTGACTTGTCCGATAAGCTTTTTACTA------------------------
upper sequence: LOC_Os05g15890.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G13180.1 (Glycine max), 3'ss of exon 6
cttagtcatttaccagcacatatacctttcacgttttaagaataatcacacttggctttggtgctttgtttatataaattgta-----taattatatgatttt--agGATGACAAAAAATTTCAAGGTGAGCTCTTTGGGATATGCAATCTGTTTCGCGACTTGTCTGATAAGCTTTTCACCAGTGAGATCATTGAAATGCATGGAG
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---------gtacca--aattctacgtattttgtttt--gcttttcttcgctttttctaaatatttattttaaaataactctaaacattaactttacttccttgcagGACTGCAAGGAATTTCAAGGAGAGCTTTTTGGGATTTCCAATTTATTTCGAGATTTATCTGATAAGTTATTTACCGGTGAGATCATTGAATTGCATGAAG
upper sequence: LOC_Os05g15890.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv12s0028g03440.t01 (Vitis vinifera), 3'ss of exon 6
---------cttagtcatttaccagcacatatacctttcacgttttaaga--ataatcacac--ttggctttggtgctttgtttatataaattgtataattatatgattttagGATGACAAAAAATTTCAAGGTGAGCTCTTTGGGATATGCAATCTGTTTCGCGACTTGTCTGATAAGCTTTTCACCAGTGAGATCATTGAAATGCATGGAG
| | | ||| | ||| ||| | | ||| | ||| | | ||||| | |||| ||| | ||| || | || | | | |||| ||| |||||||||| || || |||||||| ||||| | ||||| || | |||||||||||||| |||||||||||||| || | |||| |
gtgtggaaattgatttttttggtctctattattcctcttgattcttacatttgtgttcagaacatcagctttctttctttcttttt-taatttagaagcttctgt----tcagGACTGCAAGGAATTTCAAGGCGAACTTTTTGGGATCTGCAACTTATTTCGTGATCTATCTGATAAGCTTTTTACCAGTGAGATCATAGAGTTACATGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacacttggctttggtgctttgtttatataaattgtataattatatgattttagGATGACAAAAAATTTCAAGGTGAGCTCTTTGGGATATGCAATCTGTTTCGCGACTTGTCTGATAAGCTTTTCACCAGTGAGATCATTGAAATGCATGGAG
tgctttgtttatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttagtcatttaccagcacatatacctttcacgttttaagaataatcacacttggctttggtgctttgtttatataaattgtataattatatgattttagGATGACAAAAAATTTCAAGGTGAGCTCTTTGGGATATGCAATCTGTTTCGCGACTTGTCTGATAAGCTTTTCACCAGTGAGATCATTGAAATGCATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - ccagcac
- - - - - - - - - - - - - - - - - - -aagaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tttggtg