Sequence
atgc intronic sequence ATGC exonic sequencegtattttagaccagcgatgtttttttatcattccctgttatgttctttcaactgacatttcttgttattattttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 1
gtattttagaccagcgatgtttttttatcattccctgttatgttctttcaactgacatttcttgttattattttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG
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gtattttaactgaaagatgtaccctc----tttcctgctatgaaccttcaactgatatttctc-------ctatattgaagTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATG
upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G34610.1 (Glycine max), 3'ss of exon 3
-------gtattttagaccagcg---atgtttttttatcattccctgttatgttctttca---actgacatttcttgttattattttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG
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gttccacatcttgtcgatcattctgtaaccttattcgtcatacattgtttgattattatgtatataattattctctaattttcctttttggcagTCATTACGAAAAATGAATCACCCAAATATTGTGAAGCTGAAAGAAGTTATTCGAGAAAGTGATATCTTGTACTTTGTTTTTGAGTACATG
upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G19110.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattttagaccagcgatgtttttttatcattccctgttatgttctttcaactgacatttcttgttattattttgttgaagTCTTTGC---GGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG
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--gtattgaactgcctttgtttaaatgcttttttttttcttgtttactgtatgtgtacttattcctccttttccctcctattagTCGCTCAGGAGAATGAATCATCCAAACATTGTGAAGTTGAAGGAAGTAATCCGGGAAAATGATATCCTATACTTTGTCTTTGAGTACATG
upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
-----gtattttag-accagcgatgtttttttatcattccctgttatgttctttcaactgacatttcttgttattattttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG
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gtactgtatctcattagctgaaaggttttgtttttttttttttttactgtatgttcgctgatttttttc----ttttctcattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG
upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S173_136V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------gtattttagaccagcgatgtttttttatcattccctgttatgttctttc--aactgacatttcttgtt-----------attattttgttga-agTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG
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gtatgaatccggcatattcgtacacaatttgatcctgtataaaattctggtgggaggtattcttt-gtggttgcttggccggtcatttgtgggcaggtgctccaagtgctaaaacagcaattgtggttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|47961778|gb|CN844487.1|CN844487EST: AGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAG TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
genomic: AGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAGgtattttaga ... tttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
EST:
gi|67011156|gb|CO439905.1|CO439905EST: GGGTTTGCGTGAAGTAAAG TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
genomic: GGGTTTGCGTGAAGTAAAGgtattttaga ... tttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcattccctgttatgttctttcaactgacatttcttgttattattttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG
aactgac putative branch site (score: 2)
ttatttt putative PPT
atttcttgttattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttagaccagcgatgtttttttatcattccctgttatgttctttcaactgacatttcttgttattattttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG