Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgacagttggcaccgcctggtagacggtagcgtagcgtagccttggtcttggatcgggttggtttttctttgttttaatgtaggataggttctgatgtaagttcacgggtgctggttgcagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G303465_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g61810.3 (Oryza sativa), 3'ss of exon 2
gtaagttgacagttggcaccgcctggtagacggtagcgtagcgtagccttggtcttggatcgggttggtttttctttgttttaatgtaggataggttctgatgtaagttcacgggtgctggttg---cagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT
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-------gtgagtctgcgcgggctcg-gtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctt-tgtggtttgggcggtggtgcgggatgggacagGGCGAGCGACAAATGTCAGAAGGAGAAGCGCAAGACCATCAACGGGGAAGATCTCCTCTTTGCGATGGGTACGCTTGGCTTTGAGGAGTACGTTGATCCG
upper sequence: GRMZM2G303465_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G33550.2 (Glycine max), 3'ss of exon 2
-------------------------------------------------------gtaagttgacagttggcaccgcctggtagacggtagc-gtagcgtagccttggtcttggatcgggttggtttttctttgttttaatgtaggataggttctgatgtaagttcacgggtgctggttgcagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT
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gtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttattttttgg-ggattgggggttctgagaattttttaattactgaattccacgcacgtg-gttattatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG
upper sequence: GRMZM2G303465_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G34050.1 (Glycine max), 3'ss of exon 1
---------------------------------------------gtaagttgacagt---tggcaccgcctggtagacggtagcgtagcgtagccttggtcttggatcgggttggtttttctttgttttaatgtaggataggttctgatgtaagttcacgggtgctggttgcagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT
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gtcagttagcaactatacatatccatatcaaatgttttgtttttatttagctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttattt-cggcgtgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG
upper sequence: GRMZM2G303465_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G33490.1 (Glycine max), 3'ss of exon 2
gtaagttgacagttggcaccgcctggtagacggtagcgtagcgtagccttggtcttggatcgggttggtttttctttgttttaatgtaggataggttctgatgtaagttcacgggtgctgg----ttgcagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT
| ||| || | | || | || || || | | | || || | || || || | ||| | | | || | | || | || |||||| || || || |||| || || ||||||| || ||||| || |||||||||||||||||||||||| | || |||||||| || | || |||
-------------------------------gttagtgt-gttttttttttcttctgattc--ttttctcctccgtttttcttatttatcatcg--cctgcttttaatttaaaattccttgaattctgtagGGCCTCTGATAAGTGTCAGAGAGAAAAGAGAAAGACTATTAACGGCGATGATTTGCTCTGGGCGATGGCCACTCTCGGTTTCGAGGATTATATGGATCCT
upper sequence: GRMZM2G303465_T04 (Zea mays), 3'ss of exon 1
lower sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------gtaagttgacag-ttggcaccgcctggtagacggtagcgtagcgtagccttggtcttgg----atcgggttggtttt-tctttgttttaatgt-aggataggttctgatgtaagttcacgggtgctggttg------cagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT
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gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgt-gtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttttagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCCMapped 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|31612002|gb|CD568624.1|CD568624EST: GAGACCCTGCAGGAGTGCGTCTCCGAGTTCATATCATTCGTGACCAGCGA GGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGA
genomic: GAGACCCTGCAGGAGTGCGTCTCCGAGTTCATATCATTCGTGACCAGCGAgtaagttgac ... ctggttgcagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGA
EST:
gi|19272479|gb|BM888735.1|BM888735EST: GAGACCCTGCAGGAGTGCGTCTCCGAGTTCATATCATTCGTGACCAGCGA GGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGA
genomic: GAGACCCTGCAGGAGTGCGTCTCCGAGTTCATATCATTCGTGACCAGCGAgtaagttgac ... ctggttgcagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgttttaatgtaggataggttctgatgtaagttcacgggtgctggttgcagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT
ttctgat putative branch site (score: 3)
ttttaatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgacagttggcaccgcctggtagacggtagcgtagcgtagccttggtcttggatcgggttggtttttctttgttttaatgtaggataggttctgatgtaagttcacgggtgctggttgcagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG