Sequence
atgc intronic sequence ATGC exonic sequence...tgacacttcttttaaatccttatgaaaatgaacgtttagagaaaaatcccctgcctgtgtgtttgatatctaacttcaagttattattgcttgaaatcagGTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAAGCCAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
Basic information
species | Glycine max |
transcript | GLYMA16G04400.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G04400.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G011246_T01 (Zea mays), 3'ss of exon 1
--tgacacttcttttaaatccttatgaaaatgaacgtttag-agaaaaatcccctgcctgtgtgtttgatatctaacttcaagttattattgcttgaaatcagGTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAAGCCAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
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tataaggtgtccttaacccaaaggtgagactcagcgcccgccacatgaatttactctgcgcatgaaactattctaaactgaatcaattcatgcttc---tcagGTTGTTCCAGCCTGGCTTAACTGCTTGCCAATAAAAGATGACAAGATTGAAGCTAAAGCTGTACATGAACAACTTTGCTCAATGGTGGAGAG
upper sequence: GLYMA16G04400.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM5G887631_T01 (Zea mays), 3'ss of exon 16
------tgacacttcttttaaatccttatgaaaatgaacgtttagagaaaaatcccctgcctgtgtgtttgatatctaacttcaagttattattgcttgaaatcagGTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAAGCCAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
| | | | | || | || | | | |||||| | | || | | | | || | || ||| || || |||||||||||| |||||||| | |||||||||||||||| || ||||||| || ||||| |||| || ||||| || ||||| || ||
aaagtgtattgcatggtgtcgattttgctgttagctt-tgctaggagaaagttactttgtgcatagaactagt--ccaaactgaaccaattcatgtttc---tcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAAGCTAAAGTTGTACATGGACAGCTTTGCTCCATGGTGGAGAG
upper sequence: GLYMA16G04400.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 17
tgacacttcttttaaatccttatgaaaatgaacgtttagagaaaaatcccctgcctgtgtg---tttgatatctaacttcaagttattattgcttgaaatcagGTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAAGCCAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
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---gttcaatggcgaattctaggttaagccaatctattgcaaatcccaacttacccacacagctttctaaatttttttttttttttttaatttttttgggcagATTGTTCCTGCTTGGTTAAGTTGCTTGCCTTTAAAAGGTGATTTGATTGAGGCCAAAGTTGTGCATGACCAACTATGTTCAATGGTGGAAAGMapped 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|22523477|gb|BU082288.1|BU082288EST: CTCTTGGAAAAATATGCCAATTCCATCGTGATAGCATAAATGCAGCACAG GTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAA
genomic: CTCTTGGAAAAATATGCCAATTCCATCGTGATAGCATAAATGCAGCACAGgtattttaca ... ttgaaatcagGTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAA
EST:
gi|58020652|gb|CX707394.1|CX707394EST: CTCTTGGAAAAATATGCCAATTCCATCGTGATAGCATAAATGCAGCACAG GTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAA
genomic: CTCTTGGAAAAATATGCCAATTCCATCGTGATAGCATAAATGCAGCACAGgtattttaca ... ttgaaatcagGTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcccctgcctgtgtgtttgatatctaacttcaagttattattgcttgaaatcagGTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAAGCCAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
atctaac putative branch site (score: 2)
ttcaagttattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgacacttcttttaaatccttatgaaaatgaacgtttagagaaaaatcccctgcctgtgtgtttgatatctaacttcaagttattattgcttgaaatcagGTTGTTCCTGCCTGGCTAAATTGCTTGCCTATAAAAGGTGATTTAATTGAAGCCAAGGTTGTGCATGACCAACTTTGTTCAATGGTTGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC