Sequence
atgc intronic sequence ATGC exonic sequence...agtatgcatatatagttatgtttctgttgtctttctgcatcttgcatttgtgatgtttgtacatttgagtatactttttaataaggttattctttctcagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 6
agtatgcatatatagttatgtttctgttgtctttctgcatcttgcatttgtgatgtttgtacatttgagtatactttttaataag-gttattctttct--cagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG
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---agaaaaataatgatttcttgcagttttttctgtagaaatctttgtggcattattaatagtttgctatttattaattgatgcctgttactgtgtcctgcagTCCTCTAGCCGTTTTGATGAACTACCAGATGAATTAGATCCCATTGGGAAACTTCCAGGATCATTTGATGATGGGGATCCACAAACCACGAACTTATATG
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G133308_T02 (Zea mays), 3'ss of exon 6
---agtatgcatatatagttatgtttctgttgtctttctgcatcttgcatttgtgatgtttgtacatttgagtatactttttaataaggttattctttctcagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG
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actgatgtccagctaatgagaaatttgtgtgatcattttgtagtttctatatg-aattttaata-gttttttttcattgatgcctaacattattttgtg-cagTCCTCGAGCCGGTTTGATGAACTACCAGATGAATTTGATCCGACTGGGAGATTTCCAGGATCATTTGATGATGGTGATCCTCAAACCACCAACTTATATG
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 6
----agtatgcatatatagttatgtttctgttgtctttctgcatcttgcatttgtgatgtttgtacatttgagtatactttttaataaggttattctttctcagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG
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aactgatgtccagctaatgagaaatttgtgtgatcattttgtagtttctatatgaa---ttttaatagtttctttcattgatgcttaaaattattttgtg-cagTCCTCGAGCCGGTTTGATGAACTACCAGATGAATTTGATCCGACTGGGAGATTTCCAGGATCATTTGATGATGGTGATCCTCAAACCACCAACTTATATG
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 6
-----agtatgcatatatagttatgtttctgttgtctttctgcatcttgcatttgtgatgtttgtacatttgagtatactttttaataaggttattctttctcagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG---
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aaataattatctgtatgtgcttattcttagaattttattttatttcttgtgttcactaaatttatgaagtag--------ttctactgatagttttccccttaaacagTCCAGTCGCTTTGATGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 2
agtatgcatatatagttatgtttctgttgtctttctgcatcttgcat-ttgtgatgtttgtacatttgagtatactttttaataaggttattctttctcagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG---
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---aaataattatctgtatgtgcatattcttagaattcattttatttcttgggttcactaaatatatgaa-gtacttctactgatagtttttccccttaaacagTCCAGTCGCTTTGACGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ32251 (Selaginella moellendorffii), 3'ss of exon 4
agtatgcatatatagt-tatgtttctgttgtctttctgcatcttgcatttgtgatgtttgtacat---ttgagtatactttttaataa---ggttattctttct---cagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG---
||| ||||| | || |||| |||| | |||| || | | || | | | | | ||||| | ||| | | | |||| || || | || || ||||| || || || ||||||| || |||||||||||||| |||||||||||||||||||| || || |||||||| |
-gtagttatatactatatagctttcagttggtccgcgctcgcttggggccaaaatcgtcctgcaaaagctaaacgttttcgtgaataaccggcttaccttctgtgtccagCCTCCCAGTCGTTTCGACGAGCTTCCCGAAGAA---GATCCGAACGGCAAGCTTCCTGGATCGTTTGATGATGGTGATCCACAGACGACCAATCTCTACGTTG
upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ16538 (Selaginella moellendorffii), 3'ss of exon 4
agtatgcatatatagt-tatgtttctgttgtctttctgcatcttgcatttgtgatgtttgtacat---ttgagtatactttttaataa---ggttattctttct---cagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG---
||| ||||| | || |||| |||| | |||| || | | || | | | | | ||||| | ||| | | | |||| || || | || || ||||| || || || ||||||| || |||||||||||||| |||||||||||||||||||| || || |||||||| |
-gtagttatatactatatagctttcagttggtccgcgctcgcttggggccaacatcgtcctgcaaaagctaaacgttttcgtgaataaccggcttaccttctgtgtccagCCTCCCAGTCGTTTCGACGAGCTTCCCGAAGAA---GATCCGAACGGCAAGCTTCCTGGATCGTTTGATGATGGTGATCCACAGACGACCAATCTCTACGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgtgatgtttgtacatttgagtatactttttaataaggttattctttctcagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG
ttttaat putative branch site (score: 3)
ttattctttctc putative PPT
atttgagtatactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtatgcatatatagttatgtttctgttgtctttctgcatcttgcatttgtgatgtttgtacatttgagtatactttttaataaggttattctttctcagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG
-gtatgca
- - - - - - - - - - - - tgttgtc
- - - - - - - - - - - - - - - - - ctgcatc
- - - - - - - - - - - - - - - - - - - - - -gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataagg