Sequence
atgc intronic sequence ATGC exonic sequence...acatttggtaacctcttgtctgactttgttttgacaagttgctgacccctgtgttgacaaactacggcatttgaaattttttttcttttcaataccgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
Basic information
species | Glycine max |
transcript | GLYMA20G35110.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
acatttggtaacctcttgtctgactttgttttgacaagttgctgacccc-tgtgttgacaaactacggcatttgaaattttttttcttttcaataccgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
| | | | |||| || | ||| |||| | | | |||| | | | ||||| | | | | || ||||||| || || || ||||||||||| ||||| || || || |||||||||||||||||||| || || ||||||||||| ||
---------------gtcagtaatcatttttttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtgat--cattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------acatttggtaacctcttgtctgactttgttttgacaagttgctgacccctgtgttgacaaactacggcatttgaaattttttttcttttcaataccg-------cagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
| | | || || | | || ||| | ||| | | | | | | || | || || || || | || | ||||| ||||| ||||| || || ||||||||||||||||| |||||||| |||| ||||||||||| ||||||||||||||
gtaagtttcacttattcctcatcttttcttccagagatgtggagtagtccacagtatccagtat-atttcgttattgaaagcaaattctctccattgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------acatttggtaacctcttgtctg-actttgttttgacaagttgctgacccctgtgttgacaaactacggcatttgaaattttttttcttttcaataccgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
|||| | | | | || | || || | || | | | | |||| |||| ||| || | | || | | | ||||| |||||| ||||||||||| ||||| |||||||||||||| || |||||| | |||||||||||||||||||||||||||||||
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgtt--caaa-tacagcttattaagtgaaatgc--tatcaat--tgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 5
acatttggtaacctcttgtctgactt-tgttttgacaagttgctgacccctgtgt-tgacaaactacggcatttgaaattttttttcttttcaataccgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
|| || || ||||| | | | ||||| || | ||| | || | | || || | || |||| || ||||| ||||||||||||||| || || || |||||||| ||||| || ||||| || || |||||||||||||| ||||| ||||||||
tcactttgtttcctctgttataagaaatgtttatgcaggaccctgcgctaactgcataagggtttatatcaactaaa--cttttgatattggaatactgcagGCCTATTCTACTGTTGGTACCCCTGACTACATTGCTCCAGAAGTGCTGCTTAAGAAAGGATATGGGATGGAGTGTGATTG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------acatttggtaacctcttgtctgactttgttttgacaagttgctgacccctgtgt-----tgacaaactacgg--catttgaaattttttttcttttca----ataccgca----gGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
||| || | | | | || | | || |||| || | || || || | | | ||| || ||| | | || || | |||| ||| ||||| |||||||| || || || |||||||| || ||||| || ||||||||||| ||||| ||||| ||||| ||
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
acatttggtaacctcttgtctgactttgttttgacaagttgctgacccctgtgttgacaaactacggcatttgaaattttttttcttttcaataccgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
|| | | | | || ||| || | | | || || ||||| ||||| || ||||| || || || |||||||| ||||||||||| |||||||| ||||| || ||||| ||||||||
-------------------------------------gtgcgtagcttgtacttccttttgtcccgattttt---atctaagtgttctttaa-----cagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG
upper sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
acatttggtaacctcttgtctgactttgttttgacaagttgctgacccctgtgttgacaaactacggcatttgaaattttttttcttttcaataccgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
| | ||| | | | |||| | | || | ||||| ||||| || ||||| || || || |||||||| ||||||||||| |||||||| ||||| || ||||| ||||||||
--------------------------------------------gtgcgtagcttg-tacttccttttgtcccgatttttatctaagtttcctttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccctgtgttgacaaactacggcatttgaaattttttttcttttcaataccgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
tgttgac putative branch site (score: 3)
ttttttttcttttcaa putative PPT
atttgaaatttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatttggtaacctcttgtctgactttgttttgacaagttgctgacccctgtgttgacaaactacggcatttgaaattttttttcttttcaataccgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - -cctcttg
- - - - - - - - - - -gactttg
- - - - - - - - - - - - - - - -tgacaag
- - - - - - - - - - - - - - - - - - - - - tgacccc
- - - - - - - - - - - - - - - - - - - - - - - - - -tgttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg