Sequence
atgc intronic sequence ATGC exonic sequence...gtctgaagtggtacattgatgcaaataatatcagtcatcgagggagattgggctgttaaattcgcacacattggaatgccttgacttgcatttggtgtagAGGAGTTTGTGGCGCACTCGTCCAATGTTAACTGCCTCAAGATTGGGAGGAAGACCTCGCGGGTTCTTGTCACAGGAGGAGAGGACCATAAGGTCAATCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g58130.1 (Oryza sativa), 3'ss of exon 1
gt-ctgaagtggtacattgatgcaaataatatcagtcatc-gagggagattgggctgttaaattcgcacacattggaatgccttgacttgcatttggtgtagAGGAGTTTGTGGCGCACTCGTCCAATGTTAACTGCCTCAAGATTGGGAGGAAGACCTCGCGGGTTCTTGTCACAGGAGGAGAGGACCATAAGGTCAATCT
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gtgcttatgaactgc-ctgaagattgcaacatgatttatttgggggtgattttgtgggtgaacttgcg-acattggaatgccttgacttgcgtttggcgtagAGGAGTTTGTGGCGCATTCATCCAATGTCAACTGCCTCAAGATTGGGAGGAAGACTTCACGAGTTCTCGTGACAGGAGGAGATGACCATAAGGTTAATCT
upper sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
gtctgaagtggtacattgatgcaaataatatcagtcatcgagggagattgggctgttaaattcgcacacattgg---aatgccttgact-tgcatttggtgtagAGGAGTTTGTGGCGCACTCGTCCAATGTTAACTGCCTCAAGATTGGGAGGAAGACCTCGCGGGTTCTTGTCACAGGAGGAGAGGACCATAAGGTCAATCT
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-tctgcag-atcccttctctacccttgcttcacagcattt--gttattttgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
upper sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S101_210V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtctgaagtggtacattgatgcaaataatatcagtcatcgagggagattgggctgttaaattcgcacacattggaatg--ccttgacttgcatttggtgtagAGGAGTTTGTGGCGCACTCGTCCAATGTTAACTGCCTCAAGATTGGGAGGAAGACCTCGCGGGTTCTTGTCACAGGAGGAGAGGACCATAAGGTCAATCT
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aatcttattagtctaaacactccaaattgt-tgagtcatttacgtgcttattggtgaggatattgtataattcggtttagtccttgactactaccc--ttcagAGGAGTTTGTTGCACACTCTTCCAATGTCAACTGCCTCAAGATTGGGAAGAAGTCCTCTAGGGTCTTGGTCACCGGCGGAGAGGATCACAAAGTCAACAT
upper sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ05569 (Selaginella moellendorffii), 3'ss of exon 1
gtctgaagtggtacattgatgcaaataatatcagtcatcgagggagattgggctgttaaattcgcacacattggaatgccttgacttgcatttggtgtagAGGAGTTTGTGGCGCACTCGTCCAATGTTAACTGCCTCAAGATTGGGAGGAAGACCTCGCGGGTTCTTGTCACAGGAGGAGAGGACCATAAGGTCAATCT
| ||| | ||| | | || ||| | |||| |||| ||| | |||||||||||| ||||| || ||| | || || ||||||||||| |||||||| || |||||||| ||
-----------------------------gtgagtttcttcgc---atttgatt-tttttttcagAGCTTTTGGTTGATCTTG--TTGGTGGCAATCCAGAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCT---------------------------------
upper sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ26184 (Selaginella moellendorffii), 3'ss of exon 1
gtctgaagtggtacattgatgcaaataatatcagtcatcgagggagattgggctgttaaattcgcacacattggaatgccttgacttgcatttggtgtagAGGAGTTTGTGGCGCACTCGTCCAATGTTAACTGCCTCAAGATTGGGAGGAAGACCTCGCGGGTTCTTGTCACAGGAGGAGAGGACCATAAGGTCAATCT
| ||| | ||| || | | ||| | |||| |||| ||| | |||||||||||| ||||| || ||| | || || ||||||||||| |||||||| || |||||||| || ||||| || ||||| || || ||||||||| |
-----------------------------gtgagtttcttcgc---attcggttttc--tttcagagctgttggttgatcttg--ttggtggcaatccagAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCTCGTCACCGGTGGAGACGATCACAAGGTCAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgggctgttaaattcgcacacattggaatgccttgacttgcatttggtgtagAGGAGTTTGTGGCGCACTCGTCCAATGTTAACTGCCTCAAGATTGGGAGGAAGACCTCGCGGGTTCTTGTCACAGGAGGAGAGGACCATAAGGTCAATCT
ccttgac putative branch site (score: 4)
tgttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgaagtggtacattgatgcaaataatatcagtcatcgagggagattgggctgttaaattcgcacacattggaatgccttgacttgcatttggtgtagAGGAGTTTGTGGCGCACTCGTCCAATGTTAACTGCCTCAAGATTGGGAGGAAGACCTCGCGGGTTCTTGTCACAGGAGGAGAGGACCATAAGGTCAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - tgatgca
- - - - - - - - - - - - - - - - - - - - - - - - tgggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttgca