Sequence
atgc intronic sequence ATGC exonic sequencegtacttttacatcaacagctctcaaataattttaagaaataattgatgattacatgtttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttggattcatggtgttttggattgttgttgtattgattatgtactatatggactctcactgtcgttattatgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
Basic information
species | Glycine max |
transcript | GLYMA06G05560.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g51210.2 (Oryza sativa), 3'ss of exon 3
gtacttttacatcaacagctctcaaataattttaagaaataattgatgattacatgtttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttggattcatg-gtgttttggattgttgttgtattgatta-tgtactatatggactctcactgtcgttattatgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
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--------------------------------------------------------------------------------------------------gtattacactcagttctacatgttttcttgatactatttgaacgggctaatatttcaaaccaccatgcttaattactgacaacttttttgtggacaatagGAGGGTATGGAACAATGGAGGAGTTGTTAGAGATGATAACTTGGTCACAACTTGGAATTCATGACAAACCA
upper sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g46360.2 (Oryza sativa), 3'ss of exon 4
gtacttttacatcaacagctctcaaataattttaagaaataattgatgattacatgtttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttggattcatggtgttttggattgttgttgtattgattatgtactatatggactctcactgtcgttattatgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
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--------------------------------------gtaattgataattcca-----atatatgtgagatggactga---cgatctgaaatgttcagtaccttctttctaa-catcatctatcacactagta----attgataattca--------aatgtaact-tggttattga--------tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA
upper sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g46360.3 (Oryza sativa), 3'ss of exon 4
gtacttttacatcaacagctctcaaataattttaagaaataattgatgattacatgtttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttggattcatggtgttttggattgttgttgtattgattatgtactatatggactctcactgtcgttattatgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG-----------------------------
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--------------------------------------gtaattgataattcca-----atatatgtgagatggactga---cgatctgaaatgttcagtaccttctttctaa-catcatctatcacactagta----attgataattca--------aatgtaact-tggttattga--------tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG
upper sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacttttacatcaacagctctcaaataattttaagaaataattgatgattacatgtttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttggattcatggtgttttggattgttgttgta-ttgattatgtactatatggactctcactgtcgttattatgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
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--------------------------------------------------------------------------------------------------------------gtgagaaaacgctttaaaactgaatcctagctaattgt-taaagttgaaagttttggtatcaaaaac-tacggggttttgt--tcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
upper sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 4
gtacttttacatcaacagctctcaaataattttaagaaataattgatgattacatgtttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttggattcatggtgttttggattgttgttgtattgattatgtactatatggactctcactgtcgttatt-atgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
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--------------------------------------------------------------------------------------------------gtaactaccttgga--cattatattccttaaagacaaaa-gtagatcatcttctatat--actcaggatactattgtttgagtttcaaattgttgt-agGAGGATATGGAACCATGGAAGAGCTGCTGGAGATGATTACATGGTCGCAACTGGGAATTCATAAAAAACCAMapped 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|193553718|gb|FK506281.1|FK506281EST: ATGCATTTGTTGCTCTCCCTG GAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAAC
genomic: ATGCATTTGTTGCTCTCCCTGgtacttttac ... ttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAAC
EST:
gi|213592624|gb|DB979415.1|DB979415EST: ATGGCTCAAGAAGCTGATGCATTTGTTGCTCTCCATT AAGGATATGGAA-CAGAGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAA
genomic: ATGGCTCAAGAAGCTGATGCATTTGTTGCTCTCCCTGgtacttttac ... ttataattagGAGGATATGGAACCA-TGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAA
EST:
gi|18734867|gb|BM528431.1|BM528431EST: GCGTAAAGCTGCCATGGCTCAAGAAGCTGATGCATTTGTTGCTCTCCCTG GAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAAC
genomic: GCGTAAAGCTGCCATGGCTCAAGAAGCTGATGCATTTGTTGCTCTCCCTGgtacttttac ... ttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattatgtactatatggactctcactgtcgttattatgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
ctctcac putative branch site (score: 3)
ttatgcctcccctt putative PPT
ttataatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttttacatcaacagctctcaaataattttaagaaataattgatgattacatgtttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttggattcatggtgttttggattgttgttgtattgattatgtactatatggactctcactgtcgttattatgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG