Sequence
atgc intronic sequence ATGC exonic sequencegtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcatatatatatgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
Basic information
species | Glycine max |
transcript | GLYMA14G21410.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcat-atatatatgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
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------------------gtctgctaacactgtt-tgatgtccttccatgctgaaagattaagatattgattta--ttgttttgtt--ttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g17350.2 (Oryza sativa), 3'ss of exon 3
gtatacatagtttcttgaatattttttcagttttctaatgtct--ctgttttcttcatatatatatgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
|||| ||| || || || | || | ||||| | || | | || || || | | | | | | || ||||||||||||||||| ||||||||||| || | ||| ||||| ||||||||||||| |||||| || | ||||||||||||||||| || || || |
gtatgtatataagtttaaac---cttaaaagttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttgagcttttagCCTGATTTTCATGTGAAAGAGAAGATCCTCACTCTGATAGACACTTGGCAAGAAGTTTTTGGCGGGGTACGTGCAAGATATCCACAATACTACGCAGCAT
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------------gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcatatatata-tgt-tgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
| | ||| | ||||||| | | ||| | | | | | || || | ||| | ||| ||| | || | | | || | | |||||||||| | ||| ||||||||||||||| | ||||| ||||| |||||||||||||||||||| || | | ||||||||||| || ||||| || || |
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaaca-aatttcttggcttgtgtttatgagta--agtaaccctattcagta-ataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcatatatatatgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
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----------gtatgtgcatacattttaaacctt--aatttactgattgtca--atagcaaatccttaatgct-tctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcatatatata------tgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
|| ||||| ||| | || | || ||| | || ||| || | | ||||| ||| | | || || ||||| || ||| |||||||| || || | || |||||||| ||||||||||| ||||| || || | ||||||||||||||||| ||||| || |
-------------gttcaatatgtttcatgcttgcaaaactctacttcttattctaatgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcatatatatatgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
| | ||||| | ||| | ||||| | || | | | || || | || | | || | | ||||| || || ||||||||||||||||| ||| | ||||| ||||| |||||||| || ||||| ||||| |||||||||||||||||||| ||||| | |
----gtaatggttcttccaaattggtctctctttctctctcccttgctctgcctctcta---atcctaat-tggtctgatgca-----tatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
gtatacatagtttcttgaatat--tttttcagttttctaatgtctctgttttcttcat---atatatatgttgatgtcatttgtcataccaa-ttgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
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gt-cagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctctgttttcttcatatatatatgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
tgttgat putative branch site (score: 4)
ttttcttcatatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcatatatatatgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT