Sequence
atgc intronic sequence ATGC exonic sequencegtagttaccacaacagctttcaaatagtttcaaagaataattgatgactgtgtgtcttatgacatgttaatgttactaaagatgctctttcatatactgaaatttactattttgatgtacttgattgctgtattgtgtatataatagtagttactatttctttcttataccctctctcatttccttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG
Basic information
species | Glycine max |
transcript | GLYMA17G34510.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g51210.2 (Oryza sativa), 3'ss of exon 3
gtagttaccacaacagctttcaaatagtttcaaagaataattgatgactgtgtgtcttatgacatgttaatgttactaaagatgctctttcatatactgaaatttac-tattttgatgtacttgattgctgtattgtgtatataatagtagttactatttctttcttataccctctctcatttccttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG
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----------------------------------------------------------------------------------------gtattacactcagttctacatgttttcttgatactatttg----aacgggctaatatttcaaaccaccatgcttaattactgacaacttt--tttgtggacaatagGAGGGTATGGAACAATGGAGGAGTTGTTAGAGATGATAACTTGGTCACAACTTGGAATTCATGACAAACCA
upper sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g46360.2 (Oryza sativa), 3'ss of exon 4
gtagttaccacaacagctttcaaatagtttcaaagaataattgatgactgtgtgtcttatgacatgttaatgttactaaagatgctctttcatatactga-aatttactattttgatgtacttgattgctg-tattgtgtat-ataatagtagttactatttctttcttataccctctctcatttccttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG
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----------------------------------------------------------gtaat-tgataattccaatatatgtgag-----atggactgacgatctgaaatgttca-gtaccttctttctaacatcatctatcacactagtaattgataattcaaatgtaa---cttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA
upper sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g46360.3 (Oryza sativa), 3'ss of exon 4
gtagttaccacaacagctttcaaatagtttcaaagaataattgatgactgtgtgtcttatgacatgttaatgttactaaagatgctctttcatatactga-aatttactattttgatgtacttgattgctg-tattgtgtat-ataatagtagttactatttctttcttataccctctctcatttccttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG-----------------------------
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----------------------------------------------------------gtaat-tgataattccaatatatgtgag-----atggactgacgatctgaaatgttca-gtaccttctttctaacatcatctatcacactagtaattgataattcaaatgtaa---cttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG
upper sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtagttaccacaacagctttcaaatagtttcaaagaataattgatgactgtgtgtcttatgacatgttaatgttactaaagatgctctttcatatactgaaatttactattttgatgtacttgattgctgtattgtgtata--taatagtagttactatttctttcttataccctctctcatttccttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG
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------------------------------------------------------------------------------------------------------------gtgagaaaacgctttaaaactgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttgtt----cagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
upper sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 4
gtagttaccacaacagctttcaaatagtttcaaagaataattgatgactgtgtgtcttatgacatgttaatgttactaaagatgctctttcatatactgaaatttactattttgatgtacttgattgctgtattgtgtatataatagtagttactatttctttcttataccctc-tctcatttcc---ttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG
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------------------------------------------------------------------------------------------------------gtaactaccttgg-acattatattccttaaagacaaaagtag-atcatcttctatatactcaggatactattgtttgagtttcaaattgttgtagGAGGATATGGAACCATGGAAGAGCTGCTGGAGATGATTACATGGTCGCAACTGGGAATTCATAAAAAACCAMapped 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|192312708|gb|FK004396.1|FK004396EST: GCGTAAAGCTGCAATGGCTCAAGAAGCTGATGCATTTATCGCCCTCCCTG GAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAAC
genomic: GCGTAAAGCTGCAATGGCTCAAGAAGCTGATGCATTTATCGCCCTCCCTGgtagttacca ... cttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAAC
EST:
gi|298195489|gb|HO043880.1|HO043880EST: GCGTAAAGCTGCAATGGCTCAAGAAGCTGATGCATTTATCGCCCTCCCTG GAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAAC
genomic: GCGTAAAGCTGCAATGGCTCAAGAAGCTGATGCATTTATCGCCCTCCCTGgtagttacca ... cttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atataatagtagttactatttctttcttataccctctctcatttccttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG
ttactatttctttctt CT-rich tract
tatttctttcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttaccacaacagctttcaaatagtttcaaagaataattgatgactgtgtgtcttatgacatgttaatgttactaaagatgctctttcatatactgaaatttactattttgatgtacttgattgctgtattgtgtatataatagtagttactatttctttcttataccctctctcatttccttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG