Sequence
atgc intronic sequence ATGC exonic sequence...aatctttgctggaactgtttaatccatgtttgctgttcttttctcactgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCATATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
Basic information
species | Glycine max |
transcript | GLYMA02G06370.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6
aatctttgctggaactgtttaatccatgtttgctgttcttttctcactgtaacta-----tgtagtgtttgatta---ctaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCAT-ATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| |||| ||| | | || ||| | ||| | | | ||| ||| | | | | | ||| |||| || || | | | |||||||||| ||||||| |||||| |||||||||||||| || || || || | ||||||||| ||||||||||| ||||||||||||||||||
----------gtaactatttcaagcttgcttgattttcatctgtgcatgtgcctaccaaatacattctgtaattgtacctaactgtttaactcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT
upper sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5
-aatctttgctggaactgtttaatccatgtttgc-tgttcttttctcactgtaactatgtagtgtt-tgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCAT-ATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| || | | || ||||| | || | || | | | | |||| || | || || | | | | ||| | |||| ||||| ||||||| |||||| || ||||||||||| || || || || | ||||||||| ||||||||||| ||||||||||||||||||
gtaactatttcaggcttgattaattttcatctgtgcaaatgcctaccattttcattctgtaagattgtacctaaatgtttaactcatttgcactatacc--agGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT
upper sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
aatctttgctggaactgtttaatccatgtttgctgttcttttctcactgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCAT-ATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| |||| ||| || | ||| | | | | || || ||| || | | || |||| | | | || || || ||||||| || ||||||| ||||| |||||||||||||||||||| || || | ||| ||||| ||||||||||| |||||||| |||||||||
----------gtaactttttcatacttgtgtacattgacctgttctttg-aacaatatgtacatcagttgctaagttgct------gttctaagcc--agGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
upper sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
aatctttgctggaactgtttaatccatgtttgctgttcttttctcactgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCAT-ATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| | || || | | | | | | || || | |||| | | | | ||| | || | |||| || || ||||||| ||||| |||||||||||||| ||||| || || | ||| ||||| ||||| ||||| |||||||| |||||||||
-------------------gtagctattttcatactcgtgtacagatctgagctttgaacaatttgtacatcagtcactaagttgc-tgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
upper sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
aatctttgctggaactgtttaatccatgtttgctgttc--ttttctcactgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCATATG-CTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| | | ||||| || | || || | | || | | | ||| | || || |||||| | | | || || || |||||||||| ||||||| ||||| || |||||||||||||| ||||| ||| | || || |||||||| || || || | |||||||||||||
-------gtacaatttctttaaacctt-ttccctatccaacattttttttcttacttt----tgctta--tactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
upper sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------aatctttgctggaactgttta-----atccatgtttgctgttcttttctcactgtaactatg-tagtgtttgattactaattggttccttgggtattatgcttt--agGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCAT-ATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| || || | | |||| ||| | || ||| ||| | | | | | | || | | ||| | ||| |||| ||| ||||||| || || |||| |||||| ||||| ||||||||||| |||||||| | ||| || ||||||||||| || ||| ||||||||||||||
gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
upper sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
---------------------aatctttgctggaactgtttaatccatgtt-tgctgttcttttc----tcactgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCATATG-CTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
||| | || | ||| |||| |||| ||||| || | | | | ||| | || || | | || | || | | | | |||||||| || ||||||| ||| || ||||| |||||||| || ||||||||| | || || || ||||||||||| |||||||| || || ||
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCATATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
tactaat putative branch site (score: 1)
tttgattactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatctttgctggaactgtttaatccatgtttgctgttcttttctcactgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCATATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - tgctgga
- - - - - - - - - - - -ccatgtt
- - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - ctatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttcc