Sequence
atgc intronic sequence ATGC exonic sequence...gttcatgcactctgctgtttggttgttacccattgttggaatttgtatgcatcaacttcagtcatgagatatgacgatgttttgaagattctgatgatagGTTGCTGCAGCTGGGTATGATAGGCAAGGAGTAGCTGATCATGCAAATAATCTTGCCTCAAAAATCAGAAGTAACTTGACCAATTCATTGAAGGGTCTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 2
--gttcatgcactctgctgtttggttgttacccattgttggaatttgtatgcatcaacttcagtcatgagatatgacgatgttttgaagattctgatgatagGTTGCTGCAGCTGGGTATGATAGGCAAGGAGTAGCTGATCATGCAAATAATCTTGCCTCAAAAATCAGAAGTAACTTGACCAATTCATTGAAGGGTCTTG
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aggcctattacctgtggcctttgggcatcggctgtt-ttctcattcttgtgtgttgcattgtgtcctgc-ataaatcattaagcccattctctgtacaacagGTTTCATCCCCTGGATATGACAGACAAGCTGTTGCTGATCATGCAAACAATCTCGCCTCTAAAATCCGAAGCAACTTGACTAATTCAATGAAAGCTCTGG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 2
---gttcatgcactctgctgtttggttgttacccattgttggaatttgtatgcatcaacttcagtcatgagatatgacgatgttttgaagattctgatgatagGTTGCTGCAGCTGGGTATGATAGGCAAGGAGTAGCTGATCATGCAAATAATCTTGCCTCAAAAATCAGAAGTAACTTGACCAATTCATTGAAGGGTCTTG
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aatatcaaaccaagaacctcctt--ttgttcatggacctttaactataagcatgttttttatggcccctaactttgctaatcattt-atcatatttgtaacagGTTTCAACAGCTGGATATGATAGGCAGGCTGTTGCAGATCATGCAAATAATCTGGCCTCTAAAATTCGTAGCAACTTGACTAATTCGATGAAAGCTTTGG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 2
-gttcatgcactctgctgtttggttgttacccattgttggaatttgtatgcatcaacttcagtcatgagatatgacgatgttttgaagattctgatgatagGTTGCTGCAGCTGGGTATGATAGGCAAGGAGTAGCTGATCATGCAAATAATCTTGCCTCAAAAATCAGAAGTAACTTGACCAATTCATTGAAGGGTCTTG
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taccttttctcttaaaccattagctatgatgtgtataccttttccctttgtatcaagtt-attcatcccttgaccctaatcatttgtgatggttgtaatagGTCTCATCACCAGGATATGACAGGCAGGTTGTTGCTGACCATGCAAATAATCTTGCATCTAAAATCCGCAGCAACTTGACTAATTCAATGAAAGCTCTGG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 2
gttcatgcactctgctgtttggttgttacccattgttggaatttgtatgcatcaacttcagtcatgagatatgacgatgttttgaagat----tctgatgatagGTTGCTGCAGCTGGGTATGATAGGCAAGGAGTAGCTGATCATGCAAATAATCTTGCCTCAAAAATCAGAAGTAACTTGACCAATTCATTGAAGGGTCTTG
||| || | | || | || | ||| ||| || | || || ||| ||| || |||| || || | | ||||| | | |||| ||||| || |||| || |||||||||||||| ||||||||||| |||||| | | |||||||| || ||| |||| | ||| |
-ctcaaccatttcttgtggtcattagcaattcttactcgaacatgt---tattatctattatcctgattgatgctgaatttttaggcatattaccttgtaacagGTTTCCTCTCCTGGATATGACAGACAAGCTGTTGCTGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgcatcaacttcagtcatgagatatgacgatgttttgaagattctgatgatagGTTGCTGCAGCTGGGTATGATAGGCAAGGAGTAGCTGATCATGCAAATAATCTTGCCTCAAAAATCAGAAGTAACTTGACCAATTCATTGAAGGGTCTTG
ttctgat putative branch site (score: 3)
atgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcatgcactctgctgtttggttgttacccattgttggaatttgtatgcatcaacttcagtcatgagatatgacgatgttttgaagattctgatgatagGTTGCTGCAGCTGGGTATGATAGGCAAGGAGTAGCTGATCATGCAAATAATCTTGCCTCAAAAATCAGAAGTAACTTGACCAATTCATTGAAGGGTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- -catgcac
- - - - - tctgctg
- - - - - - - - - -tggttgt
- - - - - - - - - - - - - - cccattg
- - - - - - - - - - - - - - - - - - - - - - gtatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - caacttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaga