Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatatatcctccactgtttttgtttcaccttcaatcaattattttttttacaaaccgcttgaattcacttacaatttcatgatttactaacgaaattgattataataatcggcgaacgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA
Basic information
species | Glycine max |
transcript | GLYMA07G36000.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 3
gtaagcatatatcctccactgtttttgtttcaccttcaatcaattattttttttacaaaccgcttgaattcacttacaatttcatgatttactaacgaaatt---gattataataatcggcgaacgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA
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----------------------------------------------------gtacgtgcctcttctggttctccattttgcatcgtttcatttgggatgtttgaaattttaactaacaatgcaatttttggttgttaattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G167276_T01 (Zea mays), 3'ss of exon 2
gtaagcatatatcctccactgtttttgtttcaccttcaatcaattattttttttacaaaccgcttgaattcacttacaatttcatgatttactaacgaaattgattataataatcggcga-acgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA
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-------------------------------------------gtatgtggtcgtcaagaagcagcagcttatt---actctttttcttcgagttctgaatcgccgagctgaaacggaggcacctgtc-tgccctg--cagACCATCCTTGGATCAAGGAAGATGGCGAAGCGCCTGACACGCCACTGGACAACGCTGTCATGAACAGGCTGAAGCAGTTCAAGGCGATGAACCAGTTCAA
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagcatatatcctccactgtttttgtttcaccttcaatcaattattttttttacaaaccgcttgaattcacttacaatttcatgatttactaacgaaat-tgattata-ataatcggcgaacgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA
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-----------------------------------------------------------------gtaagcatctacaaaatatataaaaactgtaaaagcataacaatatattatctctaatgttatcttcctttgtaaagACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G19360.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagcatatatcctccactgtttttgtttcaccttcaatcaattattttttttacaaaccgcttgaattcacttacaatttcatgatttactaacgaaattgattataataatcggcgaacgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA
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------------------------------------------------------gtaagcagctcttat---cttaaaagctccta---tatatatttcattga--actcttcttgacatttttgttgttttaaa----gATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
upper sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g03150.t01 (Vitis vinifera), 3'ss of exon 3
gtaagcatatatcctccactgtttttgtttcaccttcaatcaattattttttttacaaacc--gcttgaattcacttacaatttcatgatttactaacgaaattgattataataatcggcgaacgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA
| | | | ||| |||| | ||||| ||| |||| || | | | | | || | |||| | | | || | ||| |||||||||||||| ||||||||||| |||||||| |||| || ||||||||||| || | | ||| | ||||| || |||||||||||| | |||||
---------------------------------actgagtttggagatatttaggaaaactttgtttgaagtcatacttaattatgatgttagccattgcacatttttctgataaaattcaa---ttttttctta------gATCATCCATGGATTAAGGAGGATGGAGAAGCACCTGATACTCCTCTTGACAATGCAGTTTTTGAAAGGTTCAAACAGTTTAGAGCAATGAACAAGTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttactaacgaaattgattataataatcggcgaacgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA
taacgaaattgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatatatcctccactgtttttgtttcaccttcaatcaattattttttttacaaaccgcttgaattcacttacaatttcatgatttactaacgaaattgattataataatcggcgaacgtgttatgttaaaaacagATCATCCATGGATCAAGGAGGATGGCGAAGCACCAGATAAACCACTTGACAATGCTGTACTGAATAGGCTGAAACAATTCAGAGCAATGAACCAATTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA