Sequence
atgc intronic sequence ATGC exonic sequence...gtggttaaagtatgttctttcgactgcattaggttgtagatagttccttgtttcaccttttctccactaatgtctttagtgatatcaaatgtttcaacagTTGGCCTTTTCCTACTGGAACTGCAGTACTTTGAACATGCTTTTTGCAAATACTTGCACTAAGGATGAATAAAATGTTAAGCAACGACTGTTTAGGGACA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G068690_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g43870.1 (Oryza sativa), 3'ss of exon 1
gtggttaaagtatgttctttcgactg--cattaggttgtagatagttccttgtttcaccttttctccactaatgtctttagtgatatcaaatgtttcaacagTTGGCCTTTTCCTACTGGAACTGCAGTACTTTGAACATGCTTTTTGCAAATACTTGCACTAAGGATGAATAAAATGTTAAGCAACGACTGTTTAGGGACA
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--gggtaaagtatgttcttccagtagatcattagtctgtagatattttaccagcttcacttttctccactaatgtctttagtgatatcaaatgtttcaacagTTGGACTTTTCCTACTGGAACTGCAGTACTTTCAACATGCTTTTTGCAAATGCCTGCATTAAGGATGAATAAAATGTTAAGCACCGACTATTTAGGGACG
upper sequence: GRMZM2G068690_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g43870.4 (Oryza sativa), 3'ss of exon 1
gtggttaaagtatgttctttcgactgcattaggttgtagatagttccttgtttcaccttttctccactaatgtctttagtgatatcaaatgtttcaacagTTGGCCTTTTCCTACTGGAACTGCAGTACTTTGAACATGCTTTTTGCAAATACTTGCACTAAGGATGAATAAAATGTTAAGCAACGACTGTTTAGGGACA-----------------------------------------------------------------------------------------------
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-----------------------------------------------------------------------------------------------aacagttggacttttcctactggaactgcagtactttcaacatgctttttgcaaatgcctgcattaaggatgaataaaatgttaagcaccgactatttagGGACGCAGGAGCTTCATTCATTTTGCAAGACCACCGAAATATTGGAAGACTCACAGTCTCAAGAGATTGCACTCGATAGAACAGCGGTGGGGTCAACACT
upper sequence: GRMZM2G068690_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g43870.5 (Oryza sativa), 3'ss of exon 1
gtggttaaagtatgttctttcgactgcattaggttgtagatagttccttgtttcaccttttct-----ccactaatgtctttagtga----tatcaaatgtttcaacagTTGGCCTTTTCCTACTGGA--ACTGCAGTACTTTGAACATGCTTTTTGCAAATACTTGCACTAAGGATGAATAAAATGTTAAGCAACGACTGTTTAGGGACA
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------gacttttcctactggaactgcagtactttcaacatgctttttgcaaatgcctgcattaaggatgaataaaatgttaagcaccgactatttagggacgcagGAGCTTCATTCATTTTGCAAGACCACCGAAATATTGGAAGACTCACAGTCTCAAGAGATTGCACTC--GATAGAACAGCGGTGGGGTCAACACTTCTAAGTC---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|91872421|gb|EB402378.1|EB402378EST: GTGCTGTGCTCAGCCAGAGGTCATCGGCGCTACGCGAGCGCACTGCCTGT TTGGCCTTTTCCTACTGGAACTGCAGTACTTTGAACATGCTTTTTGCAAAT
genomic: GTGCTGTGCTCAGCCAGAGGTCATCGGCGCTACGCGAGCGCACTGCCTGTgtacgtatct ... gtttcaacagTTGGCCTTTTCCTACTGGAACTGCAGTACTTTGAACATGCTTTTTGCAAAT
EST:
gi|78083007|gb|DV511400.1|DV511400EST: GTGCTGTGCTCAGCCAGAGGTCATCGGCGCTACGCGAGCGCACTGCCTGT TTGGCCTTTTCCTACTGGAACTGCAGTACTTTGAACATGCTTTTTGCAAAT
genomic: GTGCTGTGCTCAGCCAGAGGTCATCGGCGCTACGCGAGCGCACTGCCTGTgtacgtatct ... gtttcaacagTTGGCCTTTTCCTACTGGAACTGCAGTACTTTGAACATGCTTTTTGCAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttgtttcaccttttctccactaatgtctttagtgatatcaaatgtttcaacagTTGGCCTTTTCCTACTGGAACTGCAGTACTTTGAACATGCTTTTTGCAAATACTTGCACTAAGGATGAATAAAATGTTAAGCAACGACTGTTTAGGGACA
cactaat putative branch site (score: 2)
atatcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggttaaagtatgttctttcgactgcattaggttgtagatagttccttgtttcaccttttctccactaatgtctttagtgatatcaaatgtttcaacagTTGGCCTTTTCCTACTGGAACTGCAGTACTTTGAACATGCTTTTTGCAAATACTTGCACTAAGGATGAATAAAATGTTAAGCAACGACTGTTTAGGGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - -gactgca