Sequence
atgc intronic sequence ATGC exonic sequence...atgtaagttagcatggtatcatcatcagctacatggattgtggtttattgatcacattatgttgcaagaatatttcatcattctgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTGGGACCCCCTGGAACTCCTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
Basic information
species | Glycine max |
transcript | GLYMA06G09190.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 6
atgtaagttagcatggtatcatcatcagctacatggattgtggtttattgatcacat-tatgttgcaagaatatttcatcattctgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTGGGACCCCCTGGAACTCCTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
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----gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaat-atagctaactcttatttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 6
atgtaagttagcatggtatcatcatcagctacatggattgtggtttattgatcacattatgttgcaagaatatttcatcattctgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTGGGACCCCCTGGAACTCCTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
|| | | | || |||| | | | | || |||||| || | | | ||| | | | | |||| |||| || || || |||||||| |||||||||||||||||||| || || || | || ||||| | ||||| | ||||| |||||||||||| |||
-------gtaactcgacctgctcttcagatgttccgtaagagtgtt-----tcacatggcgtctctgaagt-tttagctaataaattttgtttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 6
atgtaagttagcatggtatcatcatcagctacatggattgtggtttattgatcacattatgttgcaagaatatttcatcattctgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTGGGACCCCCTGGAACTCCTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
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-------gtgatctgctttc--tgttgttgagatggaactttttttctt-atatggttgttttaaaagtggatctcataaga-tgcgtatatgac-acagGTATGTCCATGGTGATGTGAAGCCTGAGAACTTCTTGCTTGGTCCTCCTGGTACCCCAGAGGAGAAGAAGCTTTTTCTTGTTGACCTTGGATTGG
upper sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 6
atgtaagttagcatggtatcatcatcagctacatggattgtggtttattgatcacattatgttgcaagaatatttcatcattctgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTGGGACCCCCTGGAACTCCTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
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-------gtaattttctaatatt-tctgctactgtaactctctttcttcaagtggtttttatt-------tgctaagaagcagtgctcctgtttctacagATATGTGCATGGCGATGTAAAACCAGAGAATTTTCTGCTTGGGCCTCCTGGAACTCCTGAAGAGAAAAAACTTTTCCTTGTAGACCTCGGCTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgatcacattatgttgcaagaatatttcatcattctgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTGGGACCCCCTGGAACTCCTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
tattgat putative branch site (score: 3)
aatatttcatcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtaagttagcatggtatcatcatcagctacatggattgtggtttattgatcacattatgttgcaagaatatttcatcattctgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTGGGACCCCCTGGAACTCCTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - gcatggt
- - - - - - - - - - - catcagc
- - - - - - - - - - - - - - - -catggat
- - - - - - - - - - - - - - - - - - - tgtggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctgt