Sequence
atgc intronic sequence ATGC exonic sequencegtatctaactttgaattctcctttttctgattaagctcttcctatttctatttctagtaatcaatgaatcttcttttgcagATAATTGCTATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTTGATGATGTTTACATTGTTTATGAGTTGATGGACACTGATCTTCATCAGATTA
Basic information
species | Glycine max |
transcript | GLYMA11G02420.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G02420.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
-------------------gtatctaactttgaattctcctttttctgattaagctcttcctatttctatttctagtaatcaatg-aatcttcttttgcagATAATTGCTATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTTGATGATGTTTACATTGTTTATGAGTTGATGGACACTGATCTTCATCAGATTA
| || | | | | |||| ||| | | || ||| ||| | | | | || | | ||||| ||||| || | ||| || || || || || |||| || |||| |||||||||||||||||| |||||||||||| |||||||| |||||||| |
ttccttttttttttgttgggcggtcaagagcgtgtgatacatttt-tgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
upper sequence: GLYMA11G02420.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 2
gtatctaactttg--aattct-----cctttttctgattaagctcttccta----------tttctatttctagtaatcaa--tgaatcttcttttgcagATAATTGCTATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTTGATGATGTTTACATTGTTTATGAGTTGATGGACACTGATCTTCATCAGATTA
|| | | | ||| ||| || || |||||| | | | ||| | | || || | || | | | ||| ||| | || | || | ||| |||||||| || || || | ||| ||| ||||||| |||||||| |||||| | ||||||||||||||||| || ||
gtcttttatcttggcaatactagggattgttagatgattagatagtaacaagaaacaattttttttgtgacttgtgacaaaatctagccatttttcacagGTCATCTCAATAAAGGACATCATACGGCCACCAAGGAGGGAGAACTTCAATGATGTCTACATTGTCTATGAGCTCATGGACACTGATCTTCACCACCTTC
upper sequence: GLYMA11G02420.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G11330.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatctaactttgaattctcctttttctgattaagctcttcctatttctatttctagtaatcaatgaatcttcttttgcagATAATTGCTATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTTGATGATGTTTACATTGTTTATGAGTTGATGGACACTGATCTTCATCAGATTA
| |||| | ||| ||| | | ||| | || |||||| | || || | ||| | ||| | ||| ||| | |||||||| |||| || | ||||| | || | ||||||||| || |||| |||||| ||||| |||||||||||||||||||
---gtaagttttgtactctattttcgcgg--taaacgattagagtttctagctaatgtggtc------ttgacttgtacagGTTGTTGTTATAAAAGATATCATTAGACCACCAAAGAAGGAAGATTTCGTTGATGTTTATATAGTTTTTGAGTTAATGGATACTGATCTTCATCAGATTA
upper sequence: GLYMA11G02420.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtatctaactttgaattctcctttttctgat-taagctcttcctatttctatttctagtaatcaatg----aatcttcttttgc---agATAATTGCTATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTTGATGATGTTTACATTGTTTATGAGTTGATGGACACTGATCTTCATCAGATTA
| | | || || | | | | | || || | || | | ||||| || |||| |||| || | ||||| || | ||| || |||||||| || | ||||| | || ||||||| |||||||||||||| |||||||||||||||||||||||||| |
tttgccttgttatgtttgtctgggagtgtgtgtacagttatcatgacctattttttcgcctgaaacatggaatcattgcccagttctttccttgccacagGTTATTGCCATCAAGGACATTATACGACCACCAAAGAAGGAAACTTTCAATGATGTCTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgattaagctcttcctatttctatttctagtaatcaatgaatcttcttttgcagATAATTGCTATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTTGATGATGTTTACATTGTTTATGAGTTGATGGACACTGATCTTCATCAGATTA
ttctgat putative branch site (score: 3)
tcttcttttgc putative PPT
tatttctatttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctaactttgaattctcctttttctgattaagctcttcctatttctatttctagtaatcaatgaatcttcttttgcagATAATTGCTATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTTGATGATGTTTACATTGTTTATGAGTTGATGGACACTGATCTTCATCAGATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA