Sequence
atgc intronic sequence ATGC exonic sequence...ttatgtggtgttgctatgttggaggcttttttgcccccttaaatacactcgattgattcaagtctattcttttccttattgtgagtgttggtttttcaagGTGGCGACAATGTCGACTCCTGCTAGGAAGAGGCTGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATA
Basic information
species | Glycine max |
transcript | GLYMA04G34170.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
----------------------------------------ttatgtggtgttgctatgttggaggcttttttgcccccttaaatacactcgattgattcaagtctattcttttccttattgtgagtgttggtttttcaagGTGG--CGACAATGTCGACTCCTGCTAGGAAGAGGCTGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATA
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gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatcct-tttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
upper sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
--ttatgtggtgttgctatgttggaggcttttttgcccccttaaatacactcgattgattcaagtctattcttttccttattgtgagtgttggtttttcaagGTGG--CGACAATGTCGACTCCTGCTAGGAAGAGGCTGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATA
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ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatcct-tttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
upper sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 1
ttatgtggtgttgctatgttggaggcttttttgcccccttaaatacactcgattgattca--agtctattcttttccttattgtgagtgttggtt----tttcaagGTGGCGACAATGTCGACTCCTGCTAGGAAGAGGCTGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATA
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----atcaaacag--aaggctgtggtttgtatgtatcttcaatagtgtttgagagaacaattagtgaattggggttcttttggttggtgttgattgaaatttatagGCCGTGACTATGTCGACCCCAGCTAGGAAGAGGTTGATGAGAGATTTTAAGAGGTTGCAACAGGACCCCCCTGCCGGCATCAGTGGAGCTCCCCAAGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactcgattgattcaagtctattcttttccttattgtgagtgttggtttttcaagGTGGCGACAATGTCGACTCCTGCTAGGAAGAGGCTGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATA
gattgat putative branch site (score: 4)
tttttc putative PPT
tattctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgtggtgttgctatgttggaggcttttttgcccccttaaatacactcgattgattcaagtctattcttttccttattgtgagtgttggtttttcaagGTGGCGACAATGTCGACTCCTGCTAGGAAGAGGCTGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG