Sequence
atgc intronic sequence ATGC exonic sequencegtatttttctgagatttactaaacttgttaataatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgtttatctctgtcaaacttggttttatgcttggcagGCGTGTGCTTATTTTCCCAAAGGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCCACTTTGCCCTATGGTTGGAGTAGATAT
Basic information
species | Glycine max |
transcript | GLYMA20G11300.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 3
gtatttttctgagatttactaaacttgttaataatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgtttatctctgtcaaacttg-gttttatgcttg---gcagGCGTGTGCTTATTTTCCCAAAGGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCCACTTTGCCCTATGGTTGGAGTAGATAT
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------------------gtaacatatctcgcggtcgcggt---tcctagtggaaatgcggttaccttgggacttgcttgaagcgcggagggttttgatatagatgttctgcctttgcgtgtagGCGTGTGCTGATTTTCCCTAAGGGGAACAATGTGGACCATTTCTCTATGTATTTGGATGTCGCGGACTCGGTGAATCTCCCTTATGGATGGAACCGGTAT
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 3
gtatttttctgagatttactaaacttgttaataatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgtttatctctgtcaaacttggttttatgcttggcagGCGTGTGCTTATTTTCCCAAAGGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCCACTTTGCCCTATGGTTGGAGTAGATAT
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------------------gtgagcttttggatc-tcttctcttgccactgtaactgctgacggaaacatgggtaaatgtttggtgggttttaatggatgtgctactttt-tgcttg-cagGCGTGTCCTAATTTTCCCCAAGGGGAACAATGTGGATCACTTCTCGATGTATTTGGATGTTGCAGATTCTGGGAACCTCCCATACGGGTGGAGCCGGTAT
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G426486_T01 (Zea mays), 3'ss of exon 4
gtatttttctgagatttactaaacttgttaataatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgtttatctctgtcaaacttggttttatgcttggcagGCGTGTGCTTATTTTCCCAAAGGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCCACTTTGCCCTATGGTTGGAGTAGATAT
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----------gtgaccttttggatcccttgccactg-tgaccg--ctactggaa---------gcatgggtagatgtctggagagttt-taatggacgtgct--actttttgcttg-cagGCGTGTGCTAATTTTCCCCAAGGGGAACAATGTGGATCACTTATCGTTGTATTTGGATGTTGCGGATTCTGGGAGCCTCCCATATGGGTGGAGCCGGTAT
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G551402_T01 (Zea mays), 3'ss of exon 1
gtatttttctgagatttactaaacttgttaataatg-gtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgtttatctctgtcaaacttggttttatgcttggcagGCGTGTGCTTATTTTCCCAAAGGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCCACTTTGCCCTATGGTTGGAGTAGATAT
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----------gtgagctccttatccttccactgttctgcctgcagaaaccatggagttttttccctagcccctctgttctttagagtac----tcataacatctgttgaccttcatg-cagGAGTGTGCTGATTTTCCCCAAGGGGAACAATGTGGACCACTTCTCAATGTACTTGGATGTTGCTGACTCAACCAGCCTTCCGTATGGTTGGAGCCGCTAT
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 3
------------gtatttttctgagatt-tactaaacttgttaataatggtgttct-attttcttgaatat----gctctggtatgtatacttgtt-ttcagtgtttatctc-tgtcaaacttggttttatgcttgg-cagGCGTGTGCTTATTTTCCCAAAGGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCCACTTTGCCCTATGGTTGGAGTAGATAT
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gtattttaattttttttcatccaaaatggcattattgttattattattatcatcatcatcttcattattattattgttgttgttgctataaccattattcttcatatggctagtgccaatcctcataattgatttgaacagGCGGGTGCTTATTTTTCCAAAGGGAAACAATGTTGAACATTTGTCTATGTACTTGGATGTTGCGGATTCATCAAGTTTGCCCTATGGGTGGAGTAGATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtatacttgttttcagtgtttatctctgtcaaacttggttttatgcttggcagGCGTGTGCTTATTTTCCCAAAGGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCCACTTTGCCCTATGGTTGGAGTAGATAT
ttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttttctgagatttactaaacttgttaataatggtgttctattttcttgaatatgctctggtatgtatacttgttttcagtgtttatctctgtcaaacttggttttatgcttggcagGCGTGTGCTTATTTTCCCAAAGGGAAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCCACTTTGCCCTATGGTTGGAGTAGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG