Sequence
atgc intronic sequence ATGC exonic sequencegtaagttattagtttgctatttttcttcaaggaatagcatttatttattctaaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
Basic information
species | Glycine max |
transcript | GLYMA12G33950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 5
--gtaagttattagttt---gctatttttcttcaaggaatagcatttatttattctaaacctattttccatttgtt----ctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
| | |||| | |||| || |||| | | || ||| || | ||| | | ||| || | ||||||||| ||||| || ||||||||||| ||||| ||||| |||||||| ||||||
gtatgacttatgtgaacaaggctacattacttctcttgcttgg--ttgtttgttttgaactggtctctaattgcttgctgatacagGTTGATCCTCTCACTCATCAAGTCAAGCTATGTGACTTTGGAAGTGCAAAGGTTCTG
upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 5
------gtaagttattagtttgctatttttcttcaaggaatagcatttatttattctaaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
| | || || || |||||| || | | || || ||| ||||| | | ||| | |||| |||| || || || ||||||||||||||||| |||||||| |||||| |||
gtaggtattcatgatcagattattattttgct--atgcgatggcctttgattattggctctgaactcctttcttgcaatacagGTGGATCCTCTAACTCATCAAGTCAAGCTCTGTGACTTTGGGAGCGCAAAAACACTG
upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 5
--------------gtaagttattagtttgctatttttcttcaaggaatagcatttatttattctaaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
| | ||| ||| | ||| || | ||| | | || ||| | | | || |||| | | ||||||||| ||||| ||||| |||||||||||||| ||||| |||||||||||||||
gtatgtgtcatgtggacaaggatttgttc-ttcctttgatttggtaattagttctgaattggtct---cgtcgtctctctttgatgtacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTG
upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 5
------gtaagtt--attagtttgctatttttcttcaaggaatagcatttatttattc-taaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
|| | | | || || | | |||||| | | | | || || | | || | |||| | | ||||||||| ||||| ||||| |||||||||||||| ||||| || |||||||| |||
gtacgtgtcatgtggacaaggtttcgttctttctttgatt--tggtaactagttctgagttggtctgatccttctttgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG
upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagttattagtttgctatttttcttcaaggaatagcatttattt-attctaaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
||| ||| | ||| |||| | || || | || | | ||| ||| | |||| || | ||||||||||||||||| ||||| || || ||||||||||||||||| ||||||||||| |||
gtacgttgatctattgtgggttttgtctttgg--taaccttgactagattgtaatcttattctctgtatgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG
upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttattagtttgctatttttcttcaaggaatagcatttatttattctaaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
|| | | | | | ||| || | | ||| | | | | || || |||| | |||| ||| || ||||||||| ||||||||||||| ||||||||||| ||||| ||
----gtaa--aaccctccttgtgctttcgagtcctggaattcttatgcttt---tcttttgctggtttg--catcagGTAAATCCACACACACACCAGCTCAAGCTCTGTGACTTTGGGAGTGCTAAAGTCTTG
upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttattagtttgctatttttcttcaaggaatagcatttatttattctaaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
| | | | | ||| || | | ||| |||| || | | | | |||| || |||| ||| || ||||||||| ||||||||||||| ||||||||||| ||||| ||
-------gtaaaccctccttgtgctttcgagtcctggaatt--cttatgcttttcttttgctggatttcatc---agGTAAATCCACACACACACCAGCTCAAGCTCTGTGACTTTGGGAGTGCTAAAGTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttcaaggaatagcatttatttattctaaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
ttctaaa putative branch site (score: 2)
ttttccatttgttct putative PPT
atttatttattctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttattagtttgctatttttcttcaaggaatagcatttatttattctaaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT