Sequence
atgc intronic sequence ATGC exonic sequencegtatgaacatttcaggactatgataaaagggaagaaaaaccctgttgagttttgatatacatacttattgtatggtgttacatacttattgtttggtgatgaattttgattgtgttttccagCTATTGATGCTCCGGGTGGTTTTCTATTCGAATGGTGGTCGGTTTTTTGGGATATATTCATTGCTAGGACTAATGAAAAACACTCAGAGGTTGCTGCATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G07580.1 (Glycine max), 3'ss of exon 2
----------------------------gtatgaac-atttcaggactatgataaaagggaagaaaaaccctgttgagttttgatatacatacttattg-tatggt--gttacatacttat---tgtttg-gtgatgaattttgattgtgttttccagCTATTGATGCTCCGGGTGGTTTTCTATTCGAATGGTGGTCGGTTTTTTGGGATATATTCATTGCTAGGACTAATGAAAAACACTCAGAGGTTGCTGCATC
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gtgagatgtctcaaatttgtactcttttgtacaaattgtattaactgtcggatttttttttactacttccttattttggttccgtgtgttttgttattgatttggttgcttgtgtgcgtgtgtgcgcatgcgtgtgggatggcaatgtggggttgcagCTATTGATGCCCCGGGAGGTTTTCTGTTCGAGTGGTGGTCGGTTTTCTGGGATATATTTATTGCAAGGACAAATGAAAAGCACTCAGAGGTTGCTGCATC
upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G07460.1 (Glycine max), 3'ss of exon 2
----------------gtatgaacatttcaggactatgataaaagggaagaaaaaccctgttgagttttgatatacatacttattgtatggtgttacatactta-ttgtttg-gtgatgaattttgattgtgttttccagCTATTGATGCTCCGGGTGGTTTTCTATTCGAATGGTGGTCGGTTTTTTGGGATATATTCATTGCTAGGACTAATGAAAAACACTCAGAGGTTGCTGCATC
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gtgagatgtctcaaaattgtgctcttttgtcaagttggagttaactgtggcatttttctttttactacttccattttggttttgtgtgttttgttattcatttggttgcttgtgtgtgggatggcgatgtggggttgcagCTATTGATGCCCCGGGAGGTTTTCTGTTCGAGTGGTGGTCGGTTTTCTGGGATATATTTATTGCAAGGACGAATGAGAAGCACTCAGAGGTTGCTGCTTC
upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G30910.1 (Glycine max), 3'ss of exon 2
gtatgaacatttcaggactatgataaaagggaagaaaaaccctgttgagttttgatatacatacttattgtatggtgttacatacttattgtttggtgatgaattttgattgtgtt------ttccagCTATTGATGCTCCGGGTGGTTTTCTATTCGAATGGTGGTCGGTTTTTTGGGATATATTCATTGCTAGGACTAATGAAAAACACTCAGAGGTTGCTGCATC
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---------------gtgagttacatagaaacaaagtagttcagttggattt-aatgtttctgttttttttttt---ttccattttatttgtttggttgcttttgttgatgataatgtggggttgcagCTATTGATGCACCTGGAGGATTTCTGTTCGAGTGGTGGTCGGTTTTCTGGGACATATTTATTGCTAGGACAAATGAGAAGCACTCAGAGGTTGCTGCATC
upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G16040.1 (Glycine max), 3'ss of exon 2
gtatgaacatttcaggactatgataaaagggaagaaaaaccctgttgagttttgatatacatacttattgtatggtgttacatacttattgtttggtgatgaattttgattgtgttttccagCTATTGATGCTCCGGGTGGTTTTCTATTCGAATGGTGGTCGGTTTTTTGGGATATATTCATTGCTAGGACTAATGAAAAACACTCAGAGGTTGCTGCATC
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--gtgagttacctagaaacaaagtagttatgttggatttaatatttctgcttt--ttttcccccgcattttatgggtctgactgctt-ttgtt-gatgataatgtggggttg-------cagCTATTGATGCCCCTGGAGGATTTCTGTTTGAGTGGTGGTCTGTTTTCTGGGACATATTTATTGCCAGGACTAATGAGAAGCACTCAGAGGTTGCTGCATC
upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ28239 (Selaginella moellendorffii), 3'ss of exon 2
gtatgaacatttcaggactatgataaaagggaagaaaaaccctgttgagttttgatatacatacttattgtatggtgttacatacttattgtttggtgatgaattttgattgtgttttccagCTATTGATGCTCCGGGTGGTTTTCTATTCGAATGGTGGTCGGTTTTTTGGGATATATTCATTGCTAGGACTAATGAAAAACACTCAGAGGTTGCTGCATC
| ||||| | || | | |||| ||| || || | | || ||| ||| | | ||| |||||| ||||| || || || ||| | ||||| |||||||| || ||||||||||| ||||||||| | || ||||| || ||||| ||||| || || |
--------------------------------------------gtaagttt-gtcatctcgattgattgggtggagtcacg-agtgatccttt---------tttctttggaactttgtagCTATCGATGCACCCGGGGGATTTTTGTTCGAGTGGTGGTCCGTGTTTTGGGATATCTTCATTGCTCGCACGAATGAGAAGCACTCGGAGGTGGCAGCGGC
upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ29739 (Selaginella moellendorffii), 3'ss of exon 2
gtatgaacatttcaggactatgataaaagggaagaaaaaccctgttgagttttgatatacatacttattgtatggtgttacatacttattgtttggtgatgaattttgattgtgttttccagCTATTGATGCTCCGGGTGGTTTTCTATTCGAATGGTGGTCGGTTTTTTGGGATATATTCATTGCTAGGACTAATGAAAAACACTCAGAGGTTGCTGCATC
| ||||| | || | | ||| ||| || || | | || ||| ||| | | ||| |||||| ||||| || || || ||| | ||||| |||||||| || ||||||||||| ||||||||| | || ||||| || ||||| ||||| || || |
--------------------------------------------gtaagttt-gtcatctcgattgatttggtggagtcacg-agtgatccttt---------tttctttggaactttgtagCTATCGATGCACCCGGGGGATTTTTGTTCGAGTGGTGGTCCGTGTTTTGGGATATCTTCATTGCTCGCACGAATGAGAAGCACTCGGAGGTGGCAGCGGC
upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ36173 (Selaginella moellendorffii), 3'ss of exon 2
gtatgaacatttcaggactatgataaaagggaagaaaaaccctgttgagttttgatatacatacttattgtatggtgttacatacttattgtttggtgatgaattttgattgtgttttccagCTATTGATGCTCCGGGTGGTTTTCTATTCGAATGGTGGTCGGTTTTTTGGGATATATTCATTGCTAGGACTAATGAAAAACACTCAGAGGTTGCTGCATC
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--------------------------------gtaagagctcctctccgtagagattcttgtcctcatagga----gttccattgctcctttttttc------cctttttttttcgatgcagCGATTGATGCTCCTGGTGGTTTTTTGTTCGAGTGGTGGTCCGTGTTCTGGGACATTTTCATTGCTCGTACGAATGAAAAGCACTCAGAGGTGGCTGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtatggtgttacatacttattgtttggtgatgaattttgattgtgttttccagCTATTGATGCTCCGGGTGGTTTTCTATTCGAATGGTGGTCGGTTTTTTGGGATATATTCATTGCTAGGACTAATGAAAAACACTCAGAGGTTGCTGCATC
ttttgat putative branch site (score: 4)
tgttttcc putative PPT
aattttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaacatttcaggactatgataaaagggaagaaaaaccctgttgagttttgatatacatacttattgtatggtgttacatacttattgtttggtgatgaattttgattgtgttttccagCTATTGATGCTCCGGGTGGTTTTCTATTCGAATGGTGGTCGGTTTTTTGGGATATATTCATTGCTAGGACTAATGAAAAACACTCAGAGGTTGCTGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC