Sequence
atgc intronic sequence ATGC exonic sequence...tgatctgagttctctatggttcctaagcatgttaacgtcacacataatttggtttcttcaaatctcgtgtttgactttgacatttatgtccattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
Basic information
species | Oryza sativa |
transcript | 13113.m00246 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 10
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 10
--------------------------------------------------------------tgatctgagtt----ctctatggttcctaagcatgttaacgtcacacataatttggtttcttcaaatctcgtg-tttgactttgacatttatgtc--cattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
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gtgattgttttccattgccatgcagatttgaatgcattattcgttagcaagtgtgtattgggagatatcagacaccgctcgtgggatgctgagcatgtgcacagtgcacctcattaagcactcgcttgtcctataattttcctttgtctgacatcgcatcatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGAGGTTATCAGTATTGTCGAATTGACGGAAATACAGGTGGAGAAGATCGTGATGCAT
upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
---------------------------------------------------------------tgatctgagttctctatggttcctaagcatgttaacgtcacacat-------aatttggtttcttcaaatctcgtgtttgactttgacatttatgtccattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
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gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcct--gaca--tagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 10
------------------------------------tgatc-tgagttctctatggttcctaagcatgttaacgt-----cacacataatttggtttcttcaaatctcgtgtttgactttgacatttatgtccattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
|||| ||| | | ||| || || | |||| || | || || || | | || || | || | | || || | | | | || |||||||| ||||| | || ||| | ||||||||| | ||| | || ||||| |||||||| || ||||||||||||||||| || ||||| ||||| |
gtcagttctgtcagagtgtgtgattcttgtcactgatgattgtgaataccttatattttgcaacc-tgtttttgtttgctctcatttatttctgccttttgaattttcttctgtgcct--aatttgtggtttttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT
upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
--------tgatctgagttctctatggttcctaagcatgttaacgtcacacataatttggtttcttcaaatctcgtgt-ttgactttgacatttatgtccattc-ta-cagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
| | | || ||||||| || | | | | | | | | | | ||| | | | || || || ||| || |||||||| |||||||||||||| | || ||||| || ||||| | || || ||||| ||||| || ||||||||||||||||| || || || ||||| |
gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------------------------------tgatctgagttctctatggttcctaagcatgttaacgtcacacataatttggtttct-tcaaatctcgtgttt-----gactttgacatttatgtccattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
| || | | | || | | ||| | || | |||| || | | ||| | || ||| || | || | | | | |||||||| ||| | |||| || | |||||||| | |||| |||| || | |||||| || || ||||||||||| || ||||||||||||||||| |
gtcagttgctgtctggaatcaaaatcttgagttatgcattcagatgactcctgcagaccctttttttgtatgcctgtacattattctataacctcattttcattgtatttaatgttgtatttttgtggatgggggaccttctatttaaaattcagATGACAAGGTTGCTGGACATTCTTGAAGATTACTTGATGTTTCGAGGATACCTGTATTGTCGAATTGATGGAAATACAGGGGGAGAAGATCGTGATGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttggtttcttcaaatctcgtgtttgactttgacatttatgtccattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
ctttgac putative branch site (score: 4)
tccattct putative PPT
acatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatctgagttctctatggttcctaagcatgttaacgtcacacataatttggtttcttcaaatctcgtgtttgactttgacatttatgtccattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
tgatctg
- - - - - -ctctatg
- - - - - - - - - - - - aagcatg
- - - - - - - - - - - - - - - - - - - - cacataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttga