Sequence
atgc intronic sequence ATGC exonic sequence...gaccttaattatctactagtacgaagatttgtttgttgcaatctgcacgtggataattggtgccatgtaaatcttacttggtgcattgttgaaatatcagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACCGAGCGTGCTGTGAAGACTTGGCAA
Basic information
species | Glycine max |
transcript | GLYMA20G34000.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34000.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g43420.1 (Oryza sativa), 3'ss of exon 1
---gaccttaattatctactagtacgaagatttgtttgttgcaatctgcacgtggataattggtgccatgtaaatcttacttggtgcattgttgaaatatcagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACCGAGCGTGCTGTGAAGACTTGGCAA
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tctgatcacacgcgacggcaaattggcaatgctctgcaccgtagcagttacaagactaatcggtagaatacataattt--tgagccctttgcactaacg-cagGAAGCATTGGAAAAGCTGGGTTACTATTCGGGCGAAGAAGACATGGAGTTCTCCAGCTTCTCATCTGGCACCGAACGAGCTGTGAAGACATGGCAG
upper sequence: GLYMA20G34000.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G031721_T02 (Zea mays), 3'ss of exon 1
----gaccttaattatctactagtacgaagatttgtttgttgcaatctgcacgtggataattggtgccatgtaaatcttacttggtgcattgttgaaatatcagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACCGAGCGTGCTGTGAAGACTTGGCAA----
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ccaaggaattcctatttcatcaaga-gaaaataaactagtttctcttagtaggcaattgtttgtcagtacaaaaa-ctaacagcattttctgcctgacg--cagGAAGCTTTGCAGAAGCTCGGTTTTTACTCAGGCGAGGAAGACATGGAGTACTCCAGTTTCTCGTCTGGCACCGAGCGAGCTGTCAAGACATGGCAGGTTA
upper sequence: GLYMA20G34000.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G031721_T03 (Zea mays), 3'ss of exon 2
----gaccttaattatctactagtacgaagatttgtttgttgcaatctgcacgtggataattggtgccatgtaaatcttacttggtgcattgttgaaatatcagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACCGAGCGTGCTGTGAAGACTTGGCAA
| || | | | | | ||| || | ||| | | | | | | ||| | ||| || || | || | |||||||| ||| ||| | || |||||||| |||||||||||||||||||| ||||| ||||| ||| |||||||| ||||| ||||| |||||
ccaaggaattcctatttcatcaaga-gaaaataaactagtttctcttagtaggcaattgtttgtcagtacaaaaa-ctaacagcattttctgcctgacg--cagGAAGCTTTGCAGAAGCTCGGTTTTTACTCAGGCGAGGAAGACATGGAGTACTCCAGTTTCTCGTCTGGCACCGAGCGAGCTGTCAAGACATGGCAG
upper sequence: GLYMA20G34000.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0051g00860.t01 (Vitis vinifera), 3'ss of exon 1
-gaccttaattatctactagtacgaagatttgtttgttgcaatctgcacgtggataattggtgccatgtaaatcttacttggtgcattgttgaaatatcagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACCGAGCGTGCTGTGAAGACTTGGCAA
| | || || | | | | | | || | || | ||| | | ||| | | | | ||| | ||| | ||||||||| | || ||||| ||||| ||||| |||||||| |||| | |||||||||||||||||| || ||| | ||||| || ||||||||
tgtctttctttttgttttgtttttttttctaatatgatctaacactttcctggtgatgatattccaattgggtgt-atttgaactagtgtgattttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTTTCCAGCTTCTCAAGTGGGACTGAGAGAGCTGTAAAAACTTGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacgtggataattggtgccatgtaaatcttacttggtgcattgttgaaatatcagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACCGAGCGTGCTGTGAAGACTTGGCAA
atcttac putative branch site (score: 3)
taaatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaccttaattatctactagtacgaagatttgtttgttgcaatctgcacgtggataattggtgccatgtaaatcttacttggtgcattgttgaaatatcagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACCGAGCGTGCTGTGAAGACTTGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA