Sequence
atgc intronic sequence ATGC exonic sequencegtctactctattgtcctttgcctttcaataacagtactctgaactcattcatgttttagaaattctaatcatgtacagtcattaaagtagcttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTG
Basic information
species | Glycine max |
transcript | GLYMA16G19390.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G19390.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 3'ss of exon 11
gtctactctattgtcctttgcctttcaataacagtactctgaactcattcatgttttagaaattctaatcatgtacagtcattaaagtagcttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTG
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------------gttcttcttctgtctgtagt-gtagagttatcacagcccttttct-gtagttccaaagaaaagcaatcatcca---------------------tatcacttacctttttt---cagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG
upper sequence: GLYMA16G19390.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g28200.2 (Oryza sativa), 3'ss of exon 10
gtctactctattgtcctttgcctttcaataacagtactctgaactcattcatgttttagaaattctaatcatgtacagtcattaaagtagcttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTG
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--gggcttcag-gttcttcttctgtctgtagt-gtagagttatcacagcccttttct-gtagttccaaagaaaagcaatcatcca---------------------tatcacttacctttttt---cagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG
upper sequence: GLYMA16G19390.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 11
gtctactctattgtcctttgcctttcaataacagtactctgaactcattcatgttttagaaattctaatcatgtacagtcattaaagtagc--ttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTG
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-------------------------------------gttatactctttttttttgtgtaaatatttatcattaacgtgcttctcaataacagtttcactttttttaaaaatgttttaaatttt---gtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG
upper sequence: GLYMA16G19390.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0105g00590.t01 (Vitis vinifera), 3'ss of exon 11
gtctactctattgtcctttgcctttcaataacagtactctgaactcattcatgttttagaaattctaatcatgtacagtcattaaagtagcttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTG
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gtttttcctgtc-tcttttacatgtttgcaatgtgaatat---cttatccttttactaaataatc-aatcacacatatatat---agtagttgtaacca---tttctat-ggtaattctgtttgaacagTCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGTGCTATTGACATCACTCAGTTATCAGTGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagtcattaaagtagcttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTG
tactgac putative branch site (score: 1)
ctaccttcttt putative PPT
attaaagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctactctattgtcctttgcctttcaataacagtactctgaactcattcatgttttagaaattctaatcatgtacagtcattaaagtagcttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA