Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgcttgtgaccaaaagttcttgattatattatgaagaaatcttttttatacttttaaatccattagtttatacatcttataaattgtttggttaaaatgttgtcctgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAG
Basic information
species | Glycine max |
transcript | GLYMA09G24970.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 3
gtatgtgcttgtgaccaaaagttcttgattatattatgaagaaatcttttttatacttttaaatccattagtttatacatcttataaattgtttggttaaaatgttgtcctgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAG
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---tatcctttgagtagtgtgccactgactattttattagga----ctgatcatcctttgtttctcttcaaatttgatataatataattctct----------gtcatttgtatcagTGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAG
upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
gtatgtgcttgtgaccaaa-agttcttgattatattatgaagaaatcttttttatacttttaaatccattagtttatacatcttataaattgtttggttaaaatgttgtcctgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAG
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-----------taatctaacggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaa-ttgttt------attgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 2
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
gtatgtgcttgtgaccaaaagttcttgattatattatgaagaaatcttttttatacttttaaatccattagtttatacatcttataaattgtttggttaaaatgttgtcctgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAG
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----------ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtc-attatttgtttccttatttgaattgttc------attatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtgcttgtgaccaaaagttcttgattatattatgaagaaatcttt---tttatacttttaaat-ccattagtttatacatcttataaattgtttggttaaaatgttgtcctg-tgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAG
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---------------------cttatgat-atctaagcaattgatttgcgactccatgtttttaaatgttgatcttttactggatttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccattagtttatacatcttataaattgtttggttaaaatgttgtcctgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAG
ttgtcct CT-rich tract
ttagtttatacatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgcttgtgaccaaaagttcttgattatattatgaagaaatcttttttatacttttaaatccattagtttatacatcttataaattgtttggttaaaatgttgtcctgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA