Sequence
atgc intronic sequence ATGC exonic sequence...tgcctatcaatgatgttgtttgcctaaatcgcaacctttgacagtgtcattattcattattttaattcactcacgactcacaagtgttctttcccctcagAGTCAAAAGAATTCAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
Basic information
species | Glycine max |
transcript | GLYMA06G22870.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g49570.1 (Oryza sativa), 3'ss of exon 7
tgcctatcaatgatgttgtttgcctaaatcgcaacctttgacagtgtcattattcattattttaattcactcacgactcaca----agtgttctttcccct---cagAGTCAAAAGAATTCAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
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------ttatttagcatgtgtatatagtgca-aatttctgttagttcacccatttaacagtgaattctacttgctatttgtaacgaagagttccttatccttgccagAGTCAGAAAAGTATAAAGCTGTTATCCTCCGTATAGACAGCCCTGGTGGTGATGCTCTTGCTTCTGATCT
upper sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G122843_T02 (Zea mays), 3'ss of exon 12
tgcctatcaatgatgtt-gtttgcctaaatcgcaacctttgacagtgtcattattcattattttaattcactcacgactcacaagtgttct-ttcccctcagAGTCAAAAGAATTCAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
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ttcttatagtttatatgagcatatacatattgtgcaaactcatgttatttcaactgacaattcca--tcacttctaattatgaagcttcttgctatttgcagAATCAGAAAAGTACAAAGCTGTTATCCTACGTATAGACAGCCCTGGTGGTGATGCTCTTGCTTCTGATCT
upper sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 7
tgcctatcaatgatgttgtttgcctaaatcgcaacctttgacagtgtcattattcattattttaattcactcacgactcacaagtgttctttcccctca-gAGTCAAAAGAATTCAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
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---------gtaggtctgtttat-tacgttttcatctactagtgtgctgttgtgt-tcgtcaatagcagctcagaactt-tatttcctctttcttttgaagAGTCCAAAAAATATAAGGCTGCCATCATCCGAATTGACAGTCCAGGAGGTGATGCTCTCGCTTCTGATTT
upper sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g04690.t01 (Vitis vinifera), 3'ss of exon 3
------tgcctatcaatgatgttgtttgcctaaatcgcaacctttgacagtgtcattattcattattttaattcactcacgactcacaagtgttctttcccctcagAGTCAAAAGAATTCAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
||| ||| | | |||| | | ||| || | ||| ||| | | || || | | | | || |||| |||| |||||| || ||||||| |||||| | |||||||| |||||||||||||||||||||||||||||
ttcttttgcatatggaaaacaaattttg----acttccaatgagtgcttattacatgatttag-gtcttgctttaagc-taatgctgggcctttttttctttccagATTCAAAAAGATATAAGGCTGTTATCATTCGCATTGACAGCCCTGGAGGTGATGCTCTTGCTTCTGATTT
upper sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ14449 (Selaginella moellendorffii), 3'ss of exon 7
tgcctatcaatgatgttgtttgcctaaatcgcaacctttgacagtgtcattattcattattttaat-tcactcacgactcacaagtgttctttcccctcagAGTCAAAAGAATTCAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
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-------------------------------------------gtctttttcttgtttagacagacgttttccatttttttcttgacttcaacttatgcagAGGCCAAGAACTTTAAAGCCGTTGTTCTCAGAATTGATAGTCCTGGAGGTGATGCACTTGCATCGGACCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcattattcattattttaattcactcacgactcacaagtgttctttcccctcagAGTCAAAAGAATTCAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
gactcac putative branch site (score: 2)
tgttctttcccctc putative PPT
tattcattattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcctatcaatgatgttgtttgcctaaatcgcaacctttgacagtgtcattattcattattttaattcactcacgactcacaagtgttctttcccctcagAGTCAAAAGAATTCAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - -gatgttg
- - - - - - - - - -ttgccta
- - - - - - - - - - - - - - -cgcaacc
- - - - - - - - - - - - - - - - - - - - -cagtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtgttc