Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgcttttgaccagaagttcttgattatattatgaagaaatcttttttctacttttaaatccattagtgtatgcatcttataaattgtttggttaaaatgttgttatgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG
Basic information
species | Glycine max |
transcript | GLYMA16G30030.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 3
gtatgtgcttttgaccagaagttcttgattatattatgaagaaatcttttttctacttttaaatccattagtgtatgcatcttataaattgtttggttaaaatgttgttatgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG
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---tatcctttgagtagtgtgccactgactattttattagga-----ctgatcatcctttgtttctcttcaaatttg-atataatataattctctgtca-----tttgtat---cagTGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAG
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
gtatgtgcttttgaccagaagttcttgattatattatgaagaaatcttttttctacttttaaatccattagtgtat-gcatcttataaattgtttggttaaaatgtt----gttatgtgt---agGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG
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-------------------------taatctaacggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 3
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
gtatgtgcttttgaccagaagttcttgattatatt-atgaagaaatcttttttctacttttaaatccattagtgtatgcatcttataaattgtttggttaaaatgttgttatgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG
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----------ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttgg--tcattatttgtttccttatttgaattgttc------attatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 2
gtatgtgcttttgaccagaagttcttgattatattatgaagaaatcttttttctacttttaaatccattagtgtatgcatcttataaattgtttggttaaaatgttgttatgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG
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--atccactttccatttgagcaattt--tcaaatcatgcttaagt-----ttccgc-----aaacctttgctttgtataccctatc--ttgataccatcatctgt-attactattagTGATAGTGGTGAAATGTGCGCAATGAAAGAGGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAGAGTGCAAAGCAATTGGGGCAG
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtgcttttgaccagaagttcttgattatattatgaagaaatcttttttctacttttaaatccattagtgtatgcatcttataaattgtttggttaaaatgttgttatg-tgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG
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-------------cttatgatatctaagcaattgatttgcgactccatgtttttaaatgttgatcttttactggat-----ttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAAMapped 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|6341576|gb|AW164400.1|AW164400EST: AGCTGCTTTGCAGAGGCACATGTGGACATGTCTATGTTGGCTTTTATGAA GGAAAGTG-TGAAATGTGTGCTATGANAGAGGTA
genomic: AGCTGCTTGGCAGAGGCACATTTGGACATGTCTATGTTGGCTTTAAT-AAgtatgtgctt ... ttatgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccattagtgtatgcatcttataaattgtttggttaaaatgttgttatgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG
ttataaattgtttggt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgcttttgaccagaagttcttgattatattatgaagaaatcttttttctacttttaaatccattagtgtatgcatcttataaattgtttggttaaaatgttgttatgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA