Sequence
atgc intronic sequence ATGC exonic sequencegtactgccttttcatctttccagctgattactgcactcacaatatttgtttatttataataataaagattatcctctcaaataatttgaactgtttgatatttttgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 5
-------------gtactgccttttcat---------ctttccagctgattactgcactcacaatatttgtttatttataa---------taataaagattatcct-------ctcaaataatttgaactgtttgatatttttgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT
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gtattactcctttgtactgatttctcttaaagttatgtgtattctcttgctaaaactttagtattatctatttgtttgtaaagagaattttaccaagtgccatttaacttaaacttgagtgataccaattccttgaaatttttgcagCTTTTGTGGAAAAGATGCAGACTGGGGGTGACCTCAATCTCATTGGGCAATTCGGTGTTGGTTTCTATTCAGTATACTTGGTTGCTGACTATGTTGAAGT
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 5
gtactgccttttcatctttccagctgattactgcactcacaatatttgtttatt-tataataataaagattatcctctcaaataatttgaactgtttgatatttttgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT
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----------ggtatgtatgttgtggcacattgctgaagtagtttttgcttgtaatgtggttgggaagat----------gttaattggagctgt-----gttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG-
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 5
gtactgccttttcatctttccagctgattactgcactcacaatatttgtttatttataataataaagattatcctctcaaataatttgaactgtttgatatttttgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT
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---------gtacgtatgttgtggacattattgctgaagtaatttttgcttg--tgatgtggttgggaatatgtt-------aattggagctgtgtgttaatt---cagCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTTGTGGCCGACTATGTCGAAGT
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 5
gtactgccttttcatctttccag--ctgat-tactgcactcacaatatttgttta-tttataataataaagattatcctctcaaataatttgaactgtttgatatttttgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT
| | || || || | | || || | || || | | | || | | ||| | | ||||| | | |||||| | | | | ||| | |||||||||||| || ||||| | | || || || ||||| |||||||| ||||| ||||| ||||||||||| || | ||||| ||||||||||||||
-----gtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaat--attaatttatattttct----tttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------------------------gtactgccttttcatctttccagctgattactgcactcacaatatttgtttatttataataataaagattatcctc--tcaaataatttgaactgtttgatatttt-tgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT
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gttagcgagctggtctgcatgcgacagtaatatattaggaaacatatcctacaaaattctgtcacagttactggtatatgaatacttggaatgaaact-caccttctcagtgtataggagcactatccggataca--tatgtaactcgatcaagtctttcattaatgaaggaatgt---ctgtcttgtgtgcggtgtagCTTTCTTGGAGCAGATGCAAAAAGGAGGGGATCTCAACCTCATAGGTCAATTTGGAGTTGGTTTCTACTCTGTGTATTTGGTTGCTGATCACGTTGAAGT
upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ28825 (Selaginella moellendorffii), 3'ss of exon 5
gtactgccttttcatctttccagctgattactgcactcacaatatttgtttatttataataataaagattatcctctcaaataatttgaactgtttgatatttttgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT
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---------------------------------------------gtgctttctttgactcctttgaatt---ttgttgaacaactttga-tgttt----cttttgtagCATTTTTCGAAAAGATGCAGTCAGGAGGTGACTTAAATTTGATTGGCCAGTTTGGAGTCGGTTTCTACTCGGTGTATTTGGTCGCGGATTACGTCGAGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataataataaagattatcctctcaaataatttgaactgtttgatatttttgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT
gtttgat putative branch site (score: 5)
tattttt CT-rich tract
aaataatttgaactgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgccttttcatctttccagctgattactgcactcacaatatttgtttatttataataataaagattatcctctcaaataatttgaactgtttgatatttttgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG