Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaagactcgatatttaggagcctcagcatcatcataaaattaaagcaaatcatataatgattgctaacacatgtgatataagtattattgttgccaattttgtgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT
Basic information
species | Glycine max |
transcript | GLYMA04G43150.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
gtaaaaagactcgatatttaggagcctcagcatcatcataaaattaaagcaaatcatataatgattgctaacacatgtgatataagtattattgttgccaattttg-tgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT
||| | || | | | | ||||| | || ||| || | ||| | | | || | | |||||| || || || | | | || | ||| | | | | || || || |||| |||| | || || | || |||| ||||||||||| ||||| || ||||||||||| || || ||||| || |||||||| ||
gtagtacaacacaaaagcaccatctgttagcat----gcagcatgcttgcatttctcgtc-tgaatagcgaggcgcatgcc-tgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatca-gGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
upper sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
gtaaaaagactcgatatttaggagcctcagcatcatcataaaattaaagcaaatcatataatgattg---ctaacacatgtgatataagtattattgttgccaattttgtgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT--
| | | || || ||||| | || | | || || | |||| | | | | | | ||||| | | | | ||| |||| | ||| ||| || |||| |||| | ||||| |||| |||| ||||||||||| ||||| || ||||||||||| ||||| || || || |||||||| ||
---------------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtg-tgcttctgctgctctacttgttgc-----agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
upper sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
gtaaaaagactcgatatttaggagcctcagcatcatcataaaattaaagcaaatcatataatgattg---ctaacacatgtgatataagtattattgttgccaattttgtgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT
| | | || || ||||| | || | | || || | |||| | | | | | | ||||| | | | | ||| |||| | ||| ||| || |||| |||| | ||||| |||| |||| ||||||||||| ||||| || ||||||||||| ||||| || || || |||||||| ||
---------------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtg-tgcttctgctgctctacttgttgc-----agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
upper sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaaagactcgatatttaggagc-ctcagca-tcatcataaaattaaagcaaatcatataatgattgctaacacatgtgatataagtattattgttgccaattttgtgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT
||| | | || |||| | ||| || | | | || || || || || ||||| | | | | ||||| | ||| | ||| || || | | | || || | |||||| ||||||||||| |||| | || ||| ||||| ||||||||||||||||||||||||||||||||||||| || |||||||| |||||||| |||||
gtatgtatttaccttaattagctgtattcatcacttagttttaatttcaaataattcccataat--cccatcccccctttgatacattgatt-----tatttattaagtaatcccatgctga-------tttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
upper sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S211_67V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaaaaagactcgatatttaggagcctcagcatcatcataaaattaaagcaaatcatataatgattgctaacacatgtgatataagtattattgttgccaattttgtgttcttcaattaatattctgtgtgtttctctga--agGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT
| | | | | | ||| |||| | | || || | || || || | | |||| | | | || | | || ||||| | | ||| || || || || | ||| | | ||| | |||||||| || || ||||||||||| |||||||| ||||| || |||||||| ||
---------------------gtgacgaactgttcctcttcaat-ggtataaattgca-actggttttcagt-cacagaatccttccatcaattttgc---tctcatactcct--aacaaggttctgaactgtgatggagctagGTTGCCAATGTCGTCCATACGGCGCCGACAACGAAGGTCTTGTACTTCACAGGAGCAACCAACATTCTGTATACTTTCGGTGGCCACGCTGTTACTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attattgttgccaattttgtgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT
aattaat putative branch site (score: 3)
tgtttctct putative PPT
ttcttcaattaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaagactcgatatttaggagcctcagcatcatcataaaattaaagcaaatcatataatgattgctaacacatgtgatataagtattattgttgccaattttgtgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT