Sequence
atgc intronic sequence ATGC exonic sequencegtgaaatgagttcagttttaccttaactatttcttttgtggctgaggtaagtttctaaacctctctttttttttttatgcagAATGATCATGATCCATCAAAGTTGGTTGCGGAGACACCATGCAAGCTTCTGAGATATTTGGTTGCAGATGACAGTCATGTTGATGCTGACACACCATATG
Basic information
species | Glycine max |
transcript | GLYMA06G11120.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 20
-------------------------------------------------gtgaaatgagttcagttt-taccttaactattt-cttttgtggctgaggtaagtttctaaacctctctttttttttttatgcagAATGATCATGATCCATCAAAGTTGGTTGCGGAGACACCATGCAAGCTTCTGAGATATTTGGTTGCAGATGACAGTCATGTTGATGCTGACACACCATATG
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gtaatgatagccttgttctttttagttctagtcacggtgtttgcttgctatttgttgtatctatttaatgcattcactaattactatattagtttgcatcatcaagttaaaatggaacttctttctt--gcagAATGACCATGACCCATCAAAGTTATTAGCTGAGACACCATGCAAACTTCTTCGTTTCTTGGTTGCTGATGGTGCTCATGTTGATGCTGATGTACCATATG
upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 18
--------------------------------------------------------------------------------------------------------gtgaaatgagttcagt--tttaccttaactatttcttttgtggctgaggtaagtttctaaacctctctttttttttttatgcagAATGATCATGATCCATCAAAGTTGGTTGCGGAGACACCATGCAAGCTTCTGAGATATTTGGTTGCAGATGACAGTCATGTTGATGCTGACACACCATATG
| ||| |||| || ||| | | | | | | || || | | | ||||| |||| || ||||||||| ||||||||||||||||| | || |||||||| ||||| ||||| | | |||||||| |||| |||||||||||| || |||||| |
gtaaatactcccttcttcctttatattcttgttgtctgattgtataactttgctagattatttgtataatttattattgcatttcaccccactaacttatctttaaaagatgggttctgttgtttgcttcagcaggcgacatcaca--taagaaaattgt---gattaatctttgttttctt--gcagAATGACCATGATCCATCAAAGTTATTAGCTGAGACACCCTGCAAACTTCTTCGTTTCTTGGTTGCTGATGGTGCTCATGTTGATGCGGATGTACCATACG
upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 17
------gtgaaatgagtt--cagttttaccttaactatttcttttgtggctgaggtaagtttc-----taa---acctctctttttttttttatgcagAATGATCATGATCCATCAAAGTTGGTTGCGGAGACACCATGCAAGCTTCTGAGATATTTGGTTGCAGATGACAGTCATGTTGATGCTGACACACCATATG
|| | || | ||||||| ||| || ||| | | |||| || | ||| ||| | || || |||| || | ||||||||||||||||| || |||||| | || ||||||||||||||| | || || || ||||| |||| |||| | ||||| |||| || || ||||
gtttcaactgaacggtttttctattttaccgtaa-tacttcacgtttctctgaagtcatttttagcaataagttatctgtcaattttggcttgttcagAATGATCATGATCCTTCGAAGTTGATGGCTGAGACACCATGCAAGTTGCTAAGGTACCTGGTTTCAGACAACAGCAGTATTGATACTGATACGCCGTATG
upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 18
------------------------------------------gtgaaatgagttcagttttaccttaactatttcttttg--tggctgaggtaagtttctaaac-ctctctttttttttttatgcagAATGATCATGATCCATCAAAGTTGGTTGCGGAGACACCATGCAAGCTTCTGAGATATTTGGTTGCAGATGACAGTCATGTTGATGCTGACACACCATATG
| | ||| || ||| | |||| | ||| ||||| | || | | || | |||||||| || | | |||||||||||||||||||| ||||| || || ||||||||||||||||| || | || || | | ||| | ||||||||||||||||||||||| ||||
gtgccactaattcccttctcttcttttctatacacactcatagctatatgttttttttttcctttaaacttaatatttaagctggctaatttatttatttatttattttcttttttgttattttcagAATGATCATGATCCATCTAAGTTAGTCGCAGAGACACCATGCAAGCTGCTACGGTACTTAATCTCGGATAATAGTCATGTTGATGCTGACACACCGTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttcttttgtggctgaggtaagtttctaaacctctctttttttttttatgcagAATGATCATGATCCATCAAAGTTGGTTGCGGAGACACCATGCAAGCTTCTGAGATATTTGGTTGCAGATGACAGTCATGTTGATGCTGACACACCATATG
ttctaaa putative branch site (score: 2)
tttctaaacctctctt CT-rich tract
tctcttttttttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaatgagttcagttttaccttaactatttcttttgtggctgaggtaagtttctaaacctctctttttttttttatgcagAATGATCATGATCCATCAAAGTTGGTTGCGGAGACACCATGCAAGCTTCTGAGATATTTGGTTGCAGATGACAGTCATGTTGATGCTGACACACCATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG