Sequence
atgc intronic sequence ATGC exonic sequence...acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
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taagtaaatttgaagaaatgcgtgatgcgagatcttatagtacttagttttgtgctaaatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT-----------------------------------
upper sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G07570.2 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
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agattcagttttgaaaatttagcgttcaatcatcaattcctatgacttaatttggaaataacttatgaagttgctaagcttgcctgtacttgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATT-CATCT----------------------------------
upper sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G07690.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
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cagttttgaagatttagtgttcaattcaatcatcaattcctatgacttaatttggaaataacttatgaagttgctaagcatgcctgcacttgcttaacagATTGAAGCTACTAGTAGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTATTGTTGGAAATGTATGGATTTTTGGAGGACATT-CATCT----------------------------------
upper sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
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tttgatattttaatgtattgtttcatgattataactttcaagtattggaatatgtaatagcttatgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATT-CATCT----------------------------------
upper sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
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acatagtgtttgtaaaactgtgtttctatgcatgctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT-----------------------------------
upper sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
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tctgatagttaattattttaaacttttaacccttttttgtatccattcaataatttatatattgtatcggttaatgatgtagctgatttctgatacccagGTTCAGTGGAATGGTGGACCATTTTAAGATGGCCTTGGACTGCTTCTTTGCAGTGTGGTTTGTTGTGGGCAATGTGTGGATATTTGGAGGTCACTCTTCT-----------------------------------Mapped 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|93011693|gb|EB637213.1|EB637213EST: ACCAGTGGTATTGTTTTGCATCTTGGATGTATCTCAATTTCTTGCCCAAG TATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
genomic: ACCAGTGGTATTGTTTTGCATCTTGGATGTATCTCAATTTCTTGCCCAAGgtaactttta ... gtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
attttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - tgctggc
- - - - - - - - - - - -cacttca
- - - - - - - - - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgtg