Sequence
atgc intronic sequence ATGC exonic sequence...attgcaatattaccacttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
Basic information
species | Glycine max |
transcript | GLYMA13G16380.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
attgcaatattaccacttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
|| ||| || || |||| | | || || || || ||| | | | | ||| || | | ||| ||||| || || || || |||||||||||||||||||| || ||||||||||| |||||||||||||| || || ||||||||| | || ||||| |||
---------gtaagttttgatctgaaattattatctt--actacctgtagttggttaacatcctcaccttaaaaagattat------gaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
upper sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
attgcaatattaccacttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
|| || || | || ||| | ||||||| || || ||| | | | | | | ||| | || | | ||| ||| | || || || |||||||||||||| |||||||| || |||||||||||||||||||| ||||||||||||||||||||| | || || || |||
----gtatgctaaatctgaaattactatctttacttcttcatagttgatt--caataccatcaactca-tattacaaaattctggtcaatttctct-tagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
upper sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
attgcaatattaccacttggtcgaaacctattttttccagctggtt---gatt-ttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
||| || || |||||| | | | | | || ||| |||| |||| | || || | || | | || || ||| || || || || || |||||||||||||| |||||||| || |||||||||||||||||||| || || ||||| |||||||| | || || | |||
---------gtac-gctgaatctgaacctactatctttacatttttatagatgattcaacatcaccaactta-tgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
upper sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
attgcaatattaccacttgg--tcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
| ||| || | | ||| || | | ||| ||| || |||| || | | |||| | || |||||| | ||| | || || |||||||| ||||| || |||||||| ||||||||| | || ||||||||||| || || || || ||||| ||||| ||||| | || || | |||
-gtaagataataaaaaccagaatcggtacaaactgcttcagactgttt--tttttcctgttccg-attt--taacttatataaatgttgctttctaat--agGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
upper sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 11
--attgcaatattacc-acttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
||| | || | | | || | | ||| || || |||| | | | ||| | || | | || ||| ||| | || |||||||| || ||||||||||||||||| ||||||||||| |||||||||||||| |||||||| || || ||||||||||| | || |||||||||
atattcctgctttctttaatatttttaagtcccctgtttgtgtcttttttttttttaattttatgtctctgttctcctaattattatttt---ttcccatcagGTATGTGGCTCCAGAGTATGCAATGACTGGCCATCTTCTTGTGAAGAGTGATGTTTATAGCTATGGAGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAA
upper sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
-attgcaatattaccacttggtcgaaacct--attttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
| |||| | || || | | | | | ||||| | | | | | || ||| | || |||| | || || |||||||| || || || |||||||| |||||||| ||||| ||||||||||||||||| || || || || ||||| ||||| | ||||| | |||
ttctcttgtattctcgtttcttctattttttagatatctttggctggaccgctagcgttgttacttgattcctg---cacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA
upper sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S95_115V6.1 (Physcomitrella patens), 3'ss of exon 7
-attgcaatattaccacttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
| | ||| || || | | ||| | | | | || || | | ||| || | ||| |||| || || || || || || ||||| |||||||| || ||||||||||||||||| || |||||||| ||||| || || ||||||||||| | | ||| | |||
ttcttttacattgg-accacatctagaactaccacattaatcagaatgtcaggacttagccttggtttctgcactgacctattggttgattcaaactgcagGTACGTTGCCCCTGAGTACGCAATGACAGGACATCTTCTTGTTAAGAGCGACGTTTACAGTTATGGAGTGGTACTTCTTGAGCTCCTCTCGGGACGGAAA
upper sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S43_35V6.1 (Physcomitrella patens), 3'ss of exon 2
attgcaatattaccact---tggtcgaaacctattttttccag-ctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
|| || | || || | | | |||||| |||| ||||| || | || ||| || || || |||| || || |||||||| |||||||| || ||||| |||||| | ||||| |||||||||||||| || ||||| || || ||||| ||||| | ||||| |||||
ctttcaccttcacatctgaatatttaggatgtattttgaccagactggtaaggttgtgtcttgat-tattgacttacg---gtagtagttgatttcaactgcagGTATGTGGCCCCGGAGTACGCTATGACAGGGCATTTACTTGTGAAGAGTGATGTTTATAGTTATGGAGTGGTGCTTCTGGAGCTCCTTTCTGGACGAAAA
upper sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ34792 (Selaginella moellendorffii), 3'ss of exon 2
attgcaatattaccacttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
|| ||||| | ||| | ||| | | ||| | | | | | ||||||||||| || ||||| || ||||| || || |||||||||||||| || ||||||||||| || || || || || ||| | | | || ||||||
-------------------------------------------gtacgttttctccatctttttttttatatcttatctcatgtgttcttttctctccagTTATGTGGCACCCGAGTACGCCATGACCGGTCACCTTCTTGTTAAGAGCGACGTTTACAGCTACGGCGTGGTACTCCTCGAGTTGCTCTCGGGTAGAAAA
upper sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ23539 (Selaginella moellendorffii), 3'ss of exon 4
attgcaatattaccacttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
|| ||||| | ||| | ||| || | ||| | | | | | ||||||||||| || ||||| || ||||| || || |||||||||||||| || ||||||||||| || || || || || ||| | | | || ||||||
-------------------------------------------gtacgttttctccatcttt--ttttttgtcttatctcatgtgttcttttctctccagTTATGTGGCACCCGAGTACGCCATGACCGGTCACCTTCTTGTTAAGAGCGACGTTTACAGCTACGGCGTGGTACTCCTCGAGTTGCTCTCGGGTAGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
atatatatcttttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgcaatattaccacttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - ccacttg
- - - - - - - - - - -cgaaacc
- - - - - - - - - - - - - - - - - - - -gctggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgac