Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttaaatgggctgtagctcacataaatacctgatagtttgcttttcccaactaatgccaaggcactatatttatttctttgtcgtggtgcatgctgagttatatgtctctgactctcaaatcagGTTATTGGGCCATATCGATCTGGAAAATCTTTTCTTCTCAATCAGCTTCTCTCCCTAACATGCAATAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g08400.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G030138_T01 (Zea mays), 3'ss of exon 2
----------------------gtatgtttaaatgggctgtagctc-acataaatacctgatagtttgcttttcc-caactaatgccaaggcactatatttatttctttgtcgtggtgcatgctgagttatatgtctctgactctcaaatcagGTTATTGGGCCATATCGATCTGGAAAATCTTTTCTTCTCAATCAGCTTCTCTCCCTAACATGCAATAAAG
||| ||||| | | ||| |||| ||||| | ||||| | |||| | ||| || | || || ||| ||||| | || | | | ||| | | | | ||| ||||||||||| || ||||| || || ||||||||||||||||| || |||||||||||| |||| | || |
gtatgttcgaactttatcagtccattgtcccaatggcttattgctttacatgaatacggggtagttagttttttcataacaaacacaaacctgctgccttt---------------tgcataccaagctctgtctcttttattgtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTCTCCCTATCATGTGACAATG
upper sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G16130.1 (Glycine max), 3'ss of exon 1
gtatgtttaaatgggctgtagctcacataaatacctgatagtttgcttttcccaactaatgccaaggcactatatttatttctttgtcgtggtgcatgctgagttatatgtctctgact-ctcaaatcagGTTATTGGGCCATATCGATCTGGAAAATCTTTTCTTCTCAATCAGCTTCTCTCCCTAACATGCAATAAAG
|||| | | | | | ||| | || ||||| | | | | || | | | ||| ||| |||| | | || | | ||||||| |||||||| ||||| ||||||||||||||| | || ||||| |||||||| || | || | |||
------------------------acattgaag--taaaattgtgcagtattgaagaaatgc--gtttaattcactgtttacctgtttatgggctcagct--tttatcattttatggttgtttttatcagGTGATTGGGCCGTATCGTTCTGGAAAATCTTTTTTGCTTAATCAACTTCTCTCTCTTTCTTGTTACGAAG
upper sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G03660.1 (Glycine max), 3'ss of exon 2
gtatgtttaaatgggctgtagctcacataaatacctgatagtttgcttttccc-aactaatgccaaggcactatatttatttctttgtcgtggtgcatgctgagttatatgtctctgactctcaaatcagGTTATTGGGCCATATCGATCTGGAAAATCTTTTCTTCTCAATCAGCTTCTCTCCCTAACATGCAATAAAG
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------------------------acattgatgtaaacttgtgcagtattgaagaaatgttgttaattcactg--tttacctgtttatgg--gctcagcttttatcattttatggttgttttt--atcagGTGATTGGACCGTATCGTTCTGGAAAATCTTTTTTGCTTAATCAACTTCTCTCTCTTTCTTGTTACGAAG
upper sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtttaaatgggctgtagctcac-ataaatacctgatagtttgcttttccc---aactaatgc---caaggcactatatttatttctttgtcgtggtgcatgctgagttatatgtc-tctgactctcaaat--cagGTTATTGGGCCATATCGATCTGGAAAATCTTTTCTTCTCAATCAGCTTCTCTCCCTAACATGCAATAAAG
|||||| | || | | |||| || ||| | | || || || | | | || | | || |||||| || |||||| | | || | ||| || | || | |||| |||| ||||| |||||||| ||||||||||| ||||| |||||||||||||| || || | || || |||
gtatgtgacagtgatgtttgactcattatcaattcttcgtatgttctttctatctgaacctggttttctcggaccaagatatttgttactttgtt-tctcacgatttgcttgttatttcctttggtgttgaaatactagGTGATTGGCCCATATCGTTCTGGAAAATCATTTCTACTCAATCAGCTTCTTTCTCTTTCTTGTTATGAAG
upper sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtttaaatgggctgtagctcacataaatacctgatagtttgcttttcccaactaatgccaaggcactatatttatttctttgtcgtggtgcatgctgagttatatgtctctgactctcaaatcagGTTATTGGGCCATATCGATCTGGAAAATCTTTTCTTCTCAATCAGCTTCTCTCCCTAACATGCAATAAAG
| | ||| | | || | |||| |||||| ||| | | | | | | | || |||| | | || |||||| ||||| ||||| || ||||||||||||||| | |||||||| ||||||||||| | || || |||
--------------------------tttggttcctagttggggatactttgtgaataat-ttgtctttagatatttgtttttctttttttctctgtttttgattcaatgttgattgttgtc--ttcagGTAATTGGTCCATACCGCTCTGGAAAATCTTTTTTGCTCAATCAACTTCTCTCCCTTTCTTGTTATGAAG
upper sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S100_89V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------gtatgtttaaatgggctgtagctcacataaatacctgatagtttgcttt-------tcccaactaatgccaaggcactatatttatttctttgtcgtggtgcatgctgagttatatgtctc-----tgactctcaaat-----cagGTTATTGGGCCATATCGATCTGGAAAATCTTTTCTTCTCAATCAGCTTCTCTCCCTAACATGCAATAAAG
|||||| || | || |||| | || ||| | || | | | | ||| | || | || | | ||| | || || | | || | | ||| ||||| || || || ||||| ||||||||||| ||||| |||||||||||||| || || | |||||| |||
gtgcgtgtggaatcaaaaccatttgttgtctttactttctcctgccttccctcctttaaacaatctctgagatgtgatgat-cctgcaaagctgttttacaaggctttgaaatcctcctgtgttactgttttaaggtcccaattgcatggcagttagcattgtacataacacgaacgagttttaaacttttgcagGTCATCGGACCTTATCGTTCTGGAAAATCATTTCTCCTCAATCAGCTTCTGTCACTTTCCTGCAATGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttctttgtcgtggtgcatgctgagttatatgtctctgactctcaaatcagGTTATTGGGCCATATCGATCTGGAAAATCTTTTCTTCTCAATCAGCTTCTCTCCCTAACATGCAATAAAG
ctctgac putative branch site (score: 3)
ctctc CT-rich tract
agttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttaaatgggctgtagctcacataaatacctgatagtttgcttttcccaactaatgccaaggcactatatttatttctttgtcgtggtgcatgctgagttatatgtctctgactctcaaatcagGTTATTGGGCCATATCGATCTGGAAAATCTTTTCTTCTCAATCAGCTTCTCTCCCTAACATGCAATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT