Sequence
atgc intronic sequence ATGC exonic sequence...tgctggtttttagtgccctgctttggatttaccaagttaaaaaatttgactccatatgaaaattcaggctgaatggatcaaatggatgtttgttttacagAGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G435244_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g05490.2 (Oryza sativa), 3'ss of exon 5
tgctggtttttagtgccctgctttggatttacca--agttaa--aaaatttgactc--catatgaaaattcaggctgaatggatcaaatggatgtttgttttacagAGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAA-----
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-tctagaccttaatgtaatgtctcatagttagcatcatttgataaaagattagctcatcacatgagaattcaggctgaaatgacta--tggac---tgttttacagAAAGGATCAAGGATTGGACTAATGTGGTTGTTGCCTATGAACCTGTGTGGGCCATTGGAACTGGTAAAGTTGCTACACCAGATCAAGCACAAGAAGTAAG
upper sequence: GRMZM2G435244_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g05490.1 (Oryza sativa), 3'ss of exon 5
tgctggtttttagtgccctgctttggatttacca--agtta--aaaaatttgactc--catatgaaaattcaggctgaatggatcaaatggatgtttgttttacagAGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAA
|| | ||| || || | | ||| || | || |||| || ||| || |||| ||||||||||||| || | |||| ||||||||||| | ||||||||| |||| || || ||||||||||||||||| || ||||| |||||||||||||||||||| || |||| ||| || || |||
-tctagaccttaatgtaatgtctcatagttagcatcatttgataaaagattagctcatcacatgagaattcaggctgaaatgacta--tggac---tgttttacagAAAGGATCAAGGATTGGACTAATGTGGTTGTTGCCTATGAACCTGTGTGGGCCATTGGAACTGGTAAAGTTGCTACACCAGATCAAGCACAAGAA
upper sequence: GRMZM2G435244_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ37925 (Selaginella moellendorffii), 3'ss of exon 5
tgctggtttttagtgccctgctttggatttaccaagttaaaaaatttgactccatatgaaaattcaggctgaatggatcaaatggatgtttgttttacagAGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAA-----
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--------------------gtttgggttt--catgtttttatcttgcatccaaaacacacacccaagc---ataactct------tgtttgtg--acagACAAGGTCAAGGACTGGAAGAATGTGGTGATAGCATACGAGCCAGTGTGGGCGATTGGAACAGGAAAAGTTGCCACCCCTGCGCAGGCCCAGGAGGTCCA
upper sequence: GRMZM2G435244_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ31929 (Selaginella moellendorffii), 3'ss of exon 5
tgctggtttttagtgccctgctttggatttaccaagttaaaaaatttgactccatatgaaaattcaggctgaatggatcaaatggatgtttgttttacagAGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAA-----
||||| ||| || ||| ||| || ||| ||| || || | || | | || |||| |||| ||| |||||||||||| || || || | || || || ||||| ||||| |||||||| || |||||||||||||| || |||||||||||
--------------------gtttgggttt--catgtt------tttatcttgcatccaaagctcacactcaa-gcat--acttcttgattgt--ggcagACAAGGTCAAGGACTGGAAGAATGTGGTGATAGCATACGAGCCAGTGTGGGCGATTGGAACAGGAAAAGTTGCCACCCCTGCGCAGGCTCAGGAGGTCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgactccatatgaaaattcaggctgaatggatcaaatggatgtttgttttacagAGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAA
atttgac putative branch site (score: 4)
tttgtttt putative PPT
atatgaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctggtttttagtgccctgctttggatttaccaagttaaaaaatttgactccatatgaaaattcaggctgaatggatcaaatggatgtttgttttacagAGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
tgctggt
- - - - - - - - cctgctt
- - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - -ccatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggatg