Sequence
atgc intronic sequence ATGC exonic sequence...caggccaagttgcagccctggttataacatgtaaatgtgtatgcatgtattcttatacagattagattaacgagtatatgaacttgtatatatttgtcagGGCACATGGATCTGGTTGGCACCTGGGGTTCTAGCAAAAGATCCAAAAAATTTCCCGGAACCAGACAAGTTCAAGCCAGAGAGGTTTGACCCAAATTGTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g01100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g50530.1 (Oryza sativa), 3'ss of exon 1
-----caggccaagttgcagccctggttataacatg-taaatgtgtatgcatgtattcttatacagattagattaacgagtatatgaacttgtatatatttgtcagGGCACATGGATCTGGTTGGCACCTGGGGTTCTAGCAAAAGATCCAAAAAATTTCCCGGAACCAGACAAGTTCAAGCCAGAGAGGTTTGACCCAAATTGTG
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ggtctttccttaatattcacatttttataggacatgacaggcttgctttcatgtttcctcttatgtactacttcagtatacatttca-ttcgt-----tttttcagGGAACATGGGTGTGGATGGCACCTGGTGTCCTAGGAAAGGATCCCAAAAATTTCCCAGAGCCAGAGGTGTTCCGGCCGGAGCGCTTCGACCCAAACGGCG
upper sequence: Vv04s0008g01100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G34530.1 (Glycine max), 3'ss of exon 5
caggccaagttgcagccctggttataacatgtaaatgtgtatgcatgtattcttatacagattagattaacgagtata----tgaacttgtatatatttgtcagGGCACATGGATCTGGTTGGCACCTGGGGTTCTAGCAAAAGATCCAAAAAATTTCCCGGAACCAGACAAGTTCAAGCCAGAGAGGTTTGACCCAAATTGTG
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ttgtctcattttctttgtt--ttagtacatgtgcaaaattttccat-tgtcttgatgcagggtattttagttatgccaccactgatgttttgtacatgag-cagGGGACATGGGTATGGTTAGCTCTAGGAGTTCTAGCAAAAGATCCAAGGAATTTTCCAGAGCCTGAGAAGTTCAAACCAGAGAGGTTTGACCCCAAATGTG
upper sequence: Vv04s0008g01100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G11040.1 (Glycine max), 3'ss of exon 5
caggccaagttgcagccctggttataacatgtaaatgtgtatgcatgtattcttatacagattagattaacgagtatat----gaacttgtatatatttgtcagGGCACATGGATCTGGTTGGCACCTGGGGTTCTAGCAAAAGATCCAAAAAATTTCCCGGAACCAGACAAGTTCAAGCCAGAGAGGTTTGACCCAAATTGTG
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-gtgcaaaatttcccactttttcttgggagaggaagacat-tgtata-atcttgatgaagggttttctagttatgccatcactgatgttttgtacacgag-cagGGGACGTGGGTATGGTTAGCTCTTGGAGTTCTAGCAAAAGATCCAAGAAATTTTCCAGAGCCTGAGAAGTTTAAACCAGAGAGGTTTGACCCCAAATGTG
upper sequence: Vv04s0008g01100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G05520.1 (Glycine max), 3'ss of exon 5
-caggccaagttgcagccctggttataacatgtaaatgtgtatgcatgtattcttatacagattagattaacgagtatatgaacttgtatatat-ttgtcagGGCACATGGATCTGGTTGGCACCTGGGGTTCTAGCAAAAGATCCAAAAAATTTCCCGGAACCAGACAAGTTCAAGCCAGAGAGGTTTGACCCAAATTGTG
||| | || | | || | | | | | || | | | || ||| || | || || | ||| | ||||| || ||| ||||||| |||| ||| |||| ||||||||| || | ||| || || || |||||||||||||| || |||||||||||||| || | ||
acagaatta-ttattgtttggtatacacactcttcacaaat-cacaatcaaattaacgagtttttacttatgctgtcactaaatatggttttatgtaagcagGGGACTTGGGTCTGGTTAGCACTTGGAGTTCCAGCAAAAGACCCCAGAAACTTTCCTGAGCCAGACAAGTTCAAACCGGAGAGGTTTGACCCCAACTTTG
upper sequence: Vv04s0008g01100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G05510.1 (Glycine max), 3'ss of exon 5
---------caggccaagttgcagccctggttataacatgtaaatgtgtatgcatgtattcttatacagattagattaacga-gtatatgaacttgtatatatttgtcagGGCACATGGATCTGGTTGGCACCTGGGGTTCTAGCAAAAGATCCAAAAAATTTCCCGGAACCAGACAAGTTCAAGCCAGAGAGGTTTGACCCAAATTGTG
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caggactgtcttttttggtatacatactcttcacaaatcacaaccaaattaacgagagtttttac-----ttgtgctgacactatatatggttttgtgtatg-----cagGGGACTTGGGTCTGGTTAGCGCTTGGAGTTCCAGCAAAAGACCCCAAAAACTTTCCAGAGCCAGAAAAGTTCAAACCAGATAGGTTTGACCCCAACTGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtattcttatacagattagattaacgagtatatgaacttgtatatatttgtcagGGCACATGGATCTGGTTGGCACCTGGGGTTCTAGCAAAAGATCCAAAAAATTTCCCGGAACCAGACAAGTTCAAGCCAGAGAGGTTTGACCCAAATTGTG
gattaac putative branch site (score: 2)
tatatgaacttgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caggccaagttgcagccctggttataacatgtaaatgtgtatgcatgtattcttatacagattagattaacgagtatatgaacttgtatatatttgtcagGGCACATGGATCTGGTTGGCACCTGGGGTTCTAGCAAAAGATCCAAAAAATTTCCCGGAACCAGACAAGTTCAAGCCAGAGAGGTTTGACCCAAATTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
caggcca
- - - - - - cagccct
- - - - - - - - - - - - - -catgtaa
- - - - - - - - - - - - - - - - - - - gtatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - atacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgaac