Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgtgcttatcctaattggcatgctacaaaagcttatccaatgaagcttgtggtccattcttttttatttttattattattactattattaaattgactacactttgtgcattgcagTGTGGTGCAGAAGAACAGATGAACTAGTGGATGGACCTAATGCTTCTCACATCACACCAAAGGCCTTGGACAGGTGGGAGCAAAGATTATCTGATGTTTT
Basic information
species | Glycine max |
transcript | GLYMA08G41890.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G41890.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 2
gtatgtgt--gctta-tcctaattggcatgctacaaaagcttatccaatgaagcttgtggtccattcttttttatttttattattattactattattaaattgactacactttgtgcattgcagTGTGGTGCAGAAGAACAGATGAACTAGTGGATGGACCTAATGCTTCTCACATCACACCAAAGGCCTTGGACAGGTGGGAGCAAAGATTATCTGATGTTTT
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gtatggattagttaactattcattgatctaccagttactctcacttg-tgaaaattcagat--aacttcaattgtttgtggaattttta--attcttacctttgtt----tttgtctttggcagTATGGTGCAGAAGAACTGATGAACTGGTAGATGGCCCTAACTCGTCTTACATTACACCAAAGGCACTTGATCGATGGGAGAAGAGATTAGAAGATCTCTT
upper sequence: GLYMA08G41890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g00960.t01 (Vitis vinifera), 3'ss of exon 2
-gtatgtgtgcttatcctaattggcatgctacaaaagcttatccaatgaagcttgtggtccattcttttttatttttattattattactattattaaattgactacactttgtgcattgcagTGTGGTGCAGAAGAACAGATGAACTAGTGGATGGACCTAATGCTTCTCACATCACACCAAAGGCCTTGGACAGGTGGGAGCAAAGATTATCTGATGTTTT
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tttagctatgtttctcatcttctgtcttccacata-------ttacagagccttgagat---tgccagacaaattttcttggca--------gttgaatca--tgcattttcttc--tgcagTGTGGTGCAGAAGGACCGACGAGCTTGTGGATGGACCTAATGCTTCACACATGTCACCCAAGGCCCTTGACAGATGGGAACAAAGGTTAATTGACCTATT
upper sequence: GLYMA08G41890.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 2
gtatgtgtgcttatcctaattggcatgctacaaaagcttatccaatgaagcttgtggtccattcttttttatttttattattattactattattaaattgactacactttg---tgcattgcagTGTGGTGCAGAAGAACAGATGAACTAGTGGATGGACCTAATGCTTCTCACATCACACCAAAGGCCTTGGACAGGTGGGAGCAAAGATTATCTGATGTTTT
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---------------agagtctgggtacttcaa-----tgtccattga--ctgggcgaccagagtttaggataagagattttgccatcctctccaa--tggcctctttgtggaatgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatttttattattattactattattaaattgactacactttgtgcattgcagTGTGGTGCAGAAGAACAGATGAACTAGTGGATGGACCTAATGCTTCTCACATCACACCAAAGGCCTTGGACAGGTGGGAGCAAAGATTATCTGATGTTTT
aattgac putative branch site (score: 3)
tttttattattattac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgtgcttatcctaattggcatgctacaaaagcttatccaatgaagcttgtggtccattcttttttatttttattattattactattattaaattgactacactttgtgcattgcagTGTGGTGCAGAAGAACAGATGAACTAGTGGATGGACCTAATGCTTCTCACATCACACCAAAGGCCTTGGACAGGTGGGAGCAAAGATTATCTGATGTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG