Sequence
atgc intronic sequence ATGC exonic sequence...atcaatctttttcagctaataattttcttgtgatttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC
Basic information
species | Glycine max |
transcript | GLYMA19G42110.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
atcaatcttt---ttcagctaataattttcttgtgatttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatat-taagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
|||||| || || | || |||||| | | |||| || || | | | | | || ||| || | | |||| | | | || | | | ||||| |||||| || |||||||||||||| || |||||||| | ||||||||||| || || ||||||||||||||
----atctttgagctcctctgaaaagtttctta--gtgctacatgatttgcctttttttttatgtacgattgag--attaatac-tggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
upper sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
-atcaatctt-tttcagctaataattttcttgtgatttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTA--GCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
| ||| || || | | || | | | || || || || || || || |||| | | | | | | ||| | | | || | | | ||| | ||||| |||||||| |||||||||||||| ||||| ||||| || || ||||| || ||||| ||||||||||| ||
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgc-tgctagatacatatt-----aatgtctatgcgaatt---ggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
upper sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G173849_T01 (Zea mays), 3'ss of exon 1
atcaatctttttcagctaataattttcttgtgatttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttca------tattaagGATATAAATATGCTTTGGTTCT--AGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
| ||| | ||| ||| | || || || || | | | | | | |||| | | | || | | | || | | | || | ||||| | |||||| |||||||| ||||| || ||||| || |||||||| |||| || ||||||||||| ||||| || |||||
-----------cgacaaaatggagatattgc-attaccatgga-aaatctgttttattctgagcatactttatattttgaagtagggtagtaacgatgttcttgctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATCG
upper sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
----atcaatctttttcagctaata-attttcttgtgat-ttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
|| | | |||| |||| || |||| || | |||| | ||| | | | | |||| | | | || |||| ||| | || | ||| |||||| |||||||| ||||| || ||||| || |||||||| |||| || ||||||||||| ||||| || |||||
agacattgcattaccatggaaaatatgttttattctgatgttatcttgagcacactttatattttcaagtatgatagtaacgatgttcttgctggttca-------gATGTTTATTGGTGATGG----AGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
upper sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
--atcaatctttttcagctaataattttcttgtgatttttgttgatgaaactcattga-ctgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
|| || | ||| | || || | ||| | | |||| | | || | || | || ||| | | || | ||| | | | | ||||||||||||||| ||||| || | ||| ||||||||||| || || || |||||||| || ||||| ||||| ||
gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatattttttgaaccaaacggaaagtaactttttttagact------------tatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
upper sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------------------atcaatctttttcagctaataattttcttgtgatttttgttgatgaaactcat---tgactg--tatggggattagttattcttatattatgtcttcatattaagG----ATATAAATATGCTTTGGTTCT--AGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
| | | | | | || ||| || | ||| || || | | | | | |||| ||| ||| | ||| | || ||| ||||| | ||| | || | | |||| |||||| |||||||| ||||||||||| || || |||||||| |||| |||||||| || || |||||||| |||||
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggata-taagattttagtg--ttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
upper sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 5
atcaatctttttcagcta-ataattttcttgtgatttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTAG--CAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
| ||| | || | || | ||| | | | | || | | || | |||| | | | | | ||| || | || | || | | |||| | | | ||||||||||| |||||||||||||| || |||||||| ||||| ||||| || ||||| ||||||||||||||
--aattctctagttgccatgtagcaattatgttagtgtgatgtgtgcattctttgatctattcttttattaaatgtaaccaaacaa---cttggaat---gtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAG
upper sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 5
atcaatctttttcagctaataattttcttgtgatttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
|| ||| | | ||||| || |||| || |||||| | | |||| || | | | | | |||||| || || | ||||||||||||||||||||||||||| | || ||||| || || || |||||| | || ||
---------------------------------gttctgtgta-ggaactctttacctgtcggg----------ttcttaaactcaagcttctggttcgtcgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG
upper sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 5
atcaatctttttcagctaataattttcttgtgatttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
|| ||| | | ||||| || |||| || | |||| || | | | ||| | | ||| | || | ||| |||||| || || | ||||||||||||||||||||||||||| | || ||||| || || || |||||| | || ||
---------------------------------gttctgtgta-ggaactctttacctgtcggg----ttgttaaactcaagcttcttgttcgt--tgcagATGTTCATCGGAGATGG----AGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaactcattgactgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC
cattgac putative branch site (score: 3)
tgtcttc putative PPT
ttattcttatattatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcaatctttttcagctaataattttcttgtgatttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - - - gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - ttgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgggg