Sequence
atgc intronic sequence ATGC exonic sequence...catttaaatggatgaagtgtttctgttgtcgttgtgctattatcctttgtaactctgaattttgatgttcaattaagtttaaattaacttcaatttccagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT
Basic information
| species | Glycine max |
| transcript | GLYMA14G14990.1 |
| intron # | 7 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 8
catttaaatggatgaagtgtttctgttgtcgttgtgctattatcctttgtaactc-tgaattttg-atgttcaattaagtttaaattaacttcaattt---ccagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT
| | | | | | | ||| | || | | | |||| |||||| | || ||| | ||| || ||| ||||||||||||||||||||||| ||||| |||||||| ||||||||||| ||||| || || ||||| || |||||| | ||||||||||| ||||| |
----tgagtttac-acgcatagctggtccaacagtctagccagtttatataacgagtgaattacacaattttcattgttctcaaacctgtttttttttaatgcagGATGGAATTGAAGAATGCCGAAAACTCTGTGGTGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTT
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G052389_T02 (Zea mays), 3'ss of exon 8
catttaaatggatgaagtgtttctgttgtcgttgtgc-tattatcctttgtaactctgaattttgatgttcaattaagtttaaattaacttcaatttc-cagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT
| | || || | | | ||| | | ||| | | | || | | | || | ||||| | ||| || ||| ||||||| ||||||||||||||| || || |||||||| ||||||||| | |||||||| || |||||||| ||||| || |||||||| || ||||| |
-gtagtaggttctggtctgatggtctagtcactatatatataaacaaaggacacatttacaatccattgttgtttaaggggagatttctctctgttttgcagGATGCAATTGAAGAATGCCGAAAGCTCTGTGGTGGACATGGTTACTTGAACAGCAGTGGGCTTCCTGAGTTGTTTGCGGTCTATGTTCCCGCTTGCACTT
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 8
catttaaatggatgaagtgtttctgttgtcgttgtgc-tattatcctttgtaactctgaattttgatgttcaattaagtttaaattaacttcaatttc-cagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT
| | || || | | | ||| | | ||| | | | || | | | || | ||||| | ||| || ||| ||||||| ||||||||||||||| || || |||||||| ||||||||| | |||||||| || |||||||| ||||| || |||||||| || ||||| |
--tagtaggttctggtctgatggtctagtcactatatatataaacaaaggacacatttacaatccattgttgtttaaggggagatttctctctgttttgcagGATGCAATTGAAGAATGCCGAAAGCTCTGTGGTGGACATGGTTACTTGAACAGCAGTGGGCTTCCTGAGTTGTTTGCGGTCTATGTTCCCGCTTGCACTT
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 8
-catttaaatggatgaagtgtttctgttgtcgttgtgctattatcctttgtaactctgaattttgatgttcaattaagtttaaattaacttcaatttcc-----agGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT
|| || ||| | |||| ||| || || | | ||| | | || ||||| | ||| ||| | ||| | | | | |||||| ||||||||||| | || || ||||| || ||||||||||| |||||||| || ||||| || |||||||| ||||||||||| ||||| |
ttatctagccatatgca-tgtt-ctgatg--gtctagtcagtatgtacgatgaag--gacttttggcaattcattgttcttatggtgactcctgtcttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 7
catttaaatggatgaagtgtttctgttgtcgttgtgctattatcctttgtaactctgaattttgat-gttcaattaagtttaaattaacttcaatttccagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT
|| | | || ||||| | || ||||| || | | || | |||| || | || ||||||| ||||||||||| ||||| |||||||||| ||||| ||| | || | ||||| || ||||| || |||||||| ||||||||||| ||||| |
----------------gtatgctttcaaatcttaacttattaaaataagt-----tgaatattatcagctaaactgtgttttttttgttgttggttaaaagGATGGGATTGAAGAATGTCGTAAGTTATGTGGTGGACATGGATACTTGTGGTGTAGTGGGCTTCCTGAATTGTTTGCTGTATATGTTCCTGCTTGCACAT
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------------catttaaatggatgaagtgtttctgttgtcgttgtgctattatcctttgtaactctgaattttgatgttcaa-ttaagtttaaattaacttcaatttccagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT
| || | | | |||| | | | | | | | | | || |||| || | || || || |||| ||| | |||||||| ||||||||||| ||||| |||||||||| ||||| ||| | || ||||||| ||||| ||| | |||||||| ||||||||||||||||| |
gtaagttccagagctgatcctttatactcactagactagattgattggtttcgtttctctgaggatccaactgctcacatgttggaagtttgttccctccttgacattgtttggaggtgtatttagagttgaaaattcagcttaagggtactattgggtgcagGATGGCATTGAAGAATGTCGTAAGTTATGTGGTGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACAT
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
catttaaatggatgaag--tgtttctgttgtcgtt--gtgctattatcctttgtaactctgaat-tttgatgttcaattaagtttaaattaacttcaatttccagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT
| || ||| || | | | | | | | | | | | | | | || ||| || | ||| ||| || |||| ||| ||||||| |||||||||||||| |||||||||||||| ||||||||||| ||||| ||||| || || ||||||||||| || ||||| |||||||| || |
----tgaactattgagtcctgatcttaatagcctacaattcaagcaagttatactagtaggtatgcttggagtgctgctaattttctgttcactttgattgt-agGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtaactctgaattttgatgttcaattaagtttaaattaacttcaatttccagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT
aattaac putative branch site (score: 2)
tttcc putative PPT
aattttgatgttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttaaatggatgaagtgtttctgttgtcgttgtgctattatcctttgtaactctgaattttgatgttcaattaagtttaaattaacttcaatttccagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - tgaagtg
- - - - - - - - - - - -tgttgtc
- - - - - - - - - - - - - - - gttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - ctctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtt
