Sequence
atgc intronic sequence ATGC exonic sequence...agatttcaggtgattcatgtattgatgccaattttcctttagtcagaaagaccatctgccccaaataatgtaattcatttatctgattttccatatgcagGATTGGTTAGACATTGATTTTGGTATTTCTGAGGGTGTTGATTTTATTGCTATTTCATTTGTCAAGTCTGCTGAAGTTATTACTCATCTTAAAAGCTATA
Basic information
| species | Glycine max |
| transcript | GLYMA20G35400.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g08340.2 (Oryza sativa), 3'ss of exon 4
agatttcaggtgattcatgtatt--gatgccaattttcctttagtcagaaagaccatctgccccaaataatg-taattcatttatctgattttccatatgcagGATTGGTTAGACATTGATTTTGGTATTTCTGAGGGTGTTGATTTTATTGCTATTTCATTTGTCAAGTCTGCTGAAGTTATTACTCATCTTAAAAGCTATA
| | | || || ||| | || | || | | | | || || | |||| | |||| | | |||| | | | ||||||||||| | ||||| || ||||| |||||||| || || ||||||||||| |||| |||||||| ||||| ||||| |||| ||||| ||||||||||
aaagtcca--ccatccatttcttagaaagctttatgtggactgttaccaagagttattgttgttgagaaatgatgattcttatttctg-tgcaacttctgcagGATTGGCTTGACATAGACTTTGGAATTTCTGAAGGCGTAGATTTTATTGCAGTTTCGTTTGTCAAATCTGCAGAAGTAATTAACCATCTGAAAAGCTATA
upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G078200_T01 (Zea mays), 3'ss of exon 4
-agatttcaggtgattcatgtattgatgccaattttcctttagtcagaaagaccatctgccccaaata-atgtaattcatttatctgattttccatatgcagGATTGGTTAGACATTGATTTTGGTATTTCTGAGGGTGTTGATTTTATTGCTATTTCATTTGTCAAGTCTGCTGAAGTTATTACTCATCTTAAAAGCTATA
| || || | |||| ||||| | | || | || | | | | | || || | || | ||| | | ||||||||||| | ||||| |||||||| ||| |||| ||||||||||| || || | ||||||||||||||||||||||| |||| |||| | || || || |
tccttctcttatgtgttgcaaattgcaaccaatcattatataat--aaaggttcgtgcattacttgcagataaaaattatacttatgacctaaactttgcagGATTGGATTGACATAGATTTTGGAATTGCTGAAGGTGTTGATTTCATCGCCGTGTCATTTGTCAAGTCTGCTGAAGTAATTAATCATTTGAAGAGTTACA
upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G066290_T01 (Zea mays), 3'ss of exon 3
agatttcaggtgattcatgtattgatgccaattt---tcctttagtcagaaagaccatctgccccaaataatgtaattcatttatctgattttccatatgcagGATTGGTTAGACATTGATTTTGGTATTTCTGAGGGTGTTGATTTTATTGCTATTTCATTTGTCAAGTCTGCTGAAGTTATTACTCATCTTAAAAGCTATA
| | | ||||| | || || | || | |||| | | | || |||| || ||| || | | ||||||||||| | ||||| || ||||| ||| | || ||||| ||||| || ||| ||||||||||||||||||| ||||| |||| || | |||||||| |
---ctgccaactagagttgtatagttgtgaaatggaatcttatagtagtggacattaatatataataacaatggtgctccttttcttgtgacaacttgtgcagGATTGGCTTGACATAGACTTTGGGATTGCCGAAGGTGTAGATTTCATCGCTGTTTCATTTGTCAAGTCTGCAGAAGTAATTAGGCACTTGAAAAGCTACA
upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G22960.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------------agatttcaggtgattcatgtattgatgcca----attttcctttagtcagaaagaccatctgccccaaataatgtaattcatttatctgat-----------tttccatatgcagGATTGGTTAGACATTGATTTTGGTATTTCTGAGGGTGTTGATTTTATTGCTATTTCATTTGTCAAGTCTGCTGAAGTTATTACTCATCTTAAAAGCTATA
| | | | | || | | || | | | | |||| | | ||| || | || || | ||| ||||| | | |||| ||||| ||||| || ||||||||||| ||| |||| ||||| ||||| |||||| | || ||||||||||| |||||||| |||| ||| |||||||| |||
gtttgtaattttgtatcttccctttaagctttgaattatgattcactttacttggtaaatttgggagggatcaaagcaatggtgaagatgtacacttttggaaactagatgagtccatgttagcaaaacagatgatacctgagggaaaacatactcattttcactgatgatacctcaattctttatattcagGACTGGTTGGATATTGATTTTGGAATTGCTGAAGGTGTGGATTTCATTGCTGTATCGTTTGTCAAGTCGGCTGAAGTCATTAATCACCTTAAAAGTTATC
upper sequence: GLYMA20G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g04480.t01 (Vitis vinifera), 3'ss of exon 3
agatttcaggtgattcatgtattgatgccaattttcctttagtcagaaagaccatctgccccaaataatgtaat--tcatttatctgattttccatatgc--agGATTGGTTAGACATTGATTTTGGTATTTCTGAGGGTGTTGATTTTATTGCTATTTCATTTGTCAAGTCTGCTGAAGTTATTACTCATCTTAAAAGCTATA
|| ||| || | ||| | |||| || ||||| | | | | | ||| | | | ||| ||| | | | |||||||| | ||||| |||||||| ||| | |||||||||||||||||||| || ||||||||||||||||||||||| |||| ||||| ||||||||||
-agttcacggtcatcaa---attcaacaaaattcagtttgagtcatctaaattttttagtttcactaaaatgacagctaacaatcaagctttttctttccttagGATTGGCTGGACATAGATTTTGGGATTGCAGAGGGTGTTGATTTTATTGCAATATCATTTGTCAAGTCTGCTGAAGTGATTAAGCATCTCAAAAGCTATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaagaccatctgccccaaataatgtaattcatttatctgattttccatatgcagGATTGGTTAGACATTGATTTTGGTATTTCTGAGGGTGTTGATTTTATTGCTATTTCATTTGTCAAGTCTGCTGAAGTTATTACTCATCTTAAAAGCTATA
atctgat putative branch site (score: 4)
ttttccat CT-rich tract
aaataatgtaattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatttcaggtgattcatgtattgatgccaattttcctttagtcagaaagaccatctgccccaaataatgtaattcatttatctgattttccatatgcagGATTGGTTAGACATTGATTTTGGTATTTCTGAGGGTGTTGATTTTATTGCTATTTCATTTGTCAAGTCTGCTGAAGTTATTACTCATCTTAAAAGCTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - ggtgatt
- - - - - - - -catgtat
- - - - - - - - - - - tgatgcc
- - - - - - - - - - - - - - - - - - - - - - -gaaagac
