Sequence
atgc intronic sequence ATGC exonic sequencegtactctctctctctctctctctctctctctctctcacatcacatttttttttataaccaacaaaacaaccaccgcgtctcttccttttcttctcattttcattttccctccaaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAG
Basic information
species | Glycine max |
transcript | GLYMA16G26220.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 1
gtactctctctctctctctctctctctctctctctcacatcacatttttttttataaccaacaaaacaaccaccgcgtctcttccttttcttctcattttcattttccctccaaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAG
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---------------------gtaagcatcctccccgccttccttccttccttccttccttccg-----ccaccaccatcctcaccctcctcctc-----cgcctcccgccc------gcagTTCAACGTCCCCGATCTCCGCGTCGGCACGCTCGACTCCCTCCTCGCCCTCAGCGACGATCTCGTCAAG
upper sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 1
-----gtactctctctctctctctctctctctctctctctcacatcacatttttttttataaccaacaaaacaaccaccgcgtctcttccttttcttctcattttcattttccctccaaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAG
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gtaagagatccccttttccgacccctctccctctcactctcccgccggaatttagttc-------------------tcgcgtcgcctcaccgtat----------------ccgccatctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG
upper sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 1
gtactctctctctctctctctctctctctctctctcacatcacatttttttttataaccaacaaaacaaccaccgcgtctcttccttttcttctcattttcattttccctccaaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAG
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gtaatcctgtcgcttctcctcctccctccttccctccaatcgc-cggaaacgaatcatctagaacacaaggctggcctcgcctcgcctgac-ctgacctcc--ttccgctcctgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG
upper sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 1
gtactctctctctctctctctctctctctctctctcacatcacatttttttttataac-caacaaaacaaccaccgcgtctcttccttttcttctcattttcattttccctccaaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAG
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----------------gtacgccatccccgtatttt---tctcatctctctccataattcaaatatttcattttcttgttactagcttctctctcttttttttgtttgtct-----tttgcagTTCAATATCCCTAATCTCCGTGTAGGAACCCTAGATTCCCTATTATCCCTCAGCGATGACCTTCAGAAGMapped 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|8284235|gb|BE021794.1|BE021794EST: AATTGCAGGAACAAATCTCCAAACACTCCTTCGACACTCCTCTTTACAGA TTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTC
genomic: AATTGCAGGAACAAATCTCCAAACACTCCTTCGACACTCCTCTTTACAGAgtactctctc ... aaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTC
EST:
gi|7478411|gb|AW666255.1|AW666255EST: GACACTCCTCTTTACAGA TTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTC
genomic: GACACTCCTCTTTACAGAgtactctctc ... aaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccaccgcgtctcttccttttcttctcattttcattttccctccaaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAG
cgtctcttccttttct CT-rich tract
attttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactctctctctctctctctctctctctctctctcacatcacatttttttttataaccaacaaaacaaccaccgcgtctcttccttttcttctcattttcattttccctccaaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC