Sequence
atgc intronic sequence ATGC exonic sequence...aattggtaattttcatcttctggtttatatccatgtttcatggggagagtgcctgttcaccaaaaccagttagttaatgctttctcttgttgatgaacagGTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATTGGACGTACAGGAAGAGCATACAATTCTGGTGCTTCTGTCTCTCTG
Basic information
species | Glycine max |
transcript | GLYMA10G29360.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G29360.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G34910.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------aattggtaattttcatcttctggtttata-tccatgtttcatgggg-------agagtgcctgttcaccaaaaccagt-tagttaatgctttct-----cttgttgatgaacagGTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATTGGACGTACAGGAAGAGCATACAATTCTGGTGCTTCTGTCTCTCTG
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gtatgctacttgacttttgctaagggggttttcttttctttgtttttgtactctttgctgcttgggatattgtaagaatccttcttttctttgctctatactcttaaccttcccttaaaccttttttatgcacagGTTATAAACTTTGATATGCCTCAAAGTGTTACTGGATATATCCATCGAATTGGGCGTACAGGGAGAGCATATAGCAGCGGATCTTCCGTTTCTCTT
upper sequence: GLYMA10G29360.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0441g00010.t01 (Vitis vinifera), 3'ss of exon 8
aattggtaattttcatcttctggtttatatccatgtttcatggggagagtgcctgttcaccaa--aaccagttagttaatgctttctcttgttgatgaacagGTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATTGGACGTACAGGAAGAGCATACAATTCTGGTGCTTCTGTCTCTCTG
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gattt-tgcttgatgactgcaagttgtgaaatcagttacatgtgaaaatgacatctttggttagtattccatttaaaaacagatg-tgttgccttttaacagGTTATAAATTTCGAAATGCCTCAAAATGCTCCAGGATATGTACATCGAATTGGACGTACTGGAAGAGCATATAATACTGGTGCATCTGTATCTCTT
upper sequence: GLYMA10G29360.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0525g00010.t01 (Vitis vinifera), 3'ss of exon 2
aattggtaattttcatcttctggtttatatccatgtttcatggggagagtgcctgttcaccaa--aaccagttagttaatgctttctcttgttgatgaacagGTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATTGGACGTACAGGAAGAGCATACAATTCTGGTGCTTCTGTCTCTCTG
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gattt-tacttgatgactgccagttgtgaaatcagttacatgtgaaaatgacatccttggttagtattccatttaaaaacagatg-tgttgccttttaacagGTTATAAATTTCGAAATGCCTCAAAATGCTCCAGGATATGTACATCGAATTGGACGTACTGGAAGAGCATATAATAGTGGTGCATCTGTATCTCTTMapped 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|193707257|gb|FK644071.1|FK644071EST: GGGAATTG-CTTTAAAAATGTATACACG GTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATT
genomic: GGGAATTGACTTTAAAAATGTATACACGgcacgcaagt ... tgatgaacagGTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATT
EST:
gi|58019626|gb|CX706368.1|CX706368EST: ATTCTGAATTTGGAGTTGTAAGGGGAATTGACTTTAAAAATGTATACACG GTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATT
genomic: ATTCTGAATTTGGAGTTGTAAGGGGAATTGACTTTAAAAATGTATACACGgcacgcaagt ... tgatgaacagGTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagtgcctgttcaccaaaaccagttagttaatgctttctcttgttgatgaacagGTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATTGGACGTACAGGAAGAGCATACAATTCTGGTGCTTCTGTCTCTCTG
tgttgat putative branch site (score: 4)
tgctttctcttgtt CT-rich tract
ttagttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattggtaattttcatcttctggtttatatccatgtttcatggggagagtgcctgttcaccaaaaccagttagttaatgctttctcttgttgatgaacagGTTATAAACTTTGAAATGCCTCAGAGTGTTGCAGGATATGTACATCGAATTGGACGTACAGGAAGAGCATACAATTCTGGTGCTTCTGTCTCTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - -tcttctg
- - - - - - - - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - gggagag
- - - - - - - - - - - - - - - - - - - - - - - - -tgcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaacc