Sequence
atgc intronic sequence ATGC exonic sequence...ggttttatttgattatgtcacaagcttctgtttatgttgtaccttaattagtattacttttagattatattcccttctaagttatgtccttctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCTGAGCAG
Basic information
species | Glycine max |
transcript | GLYMA11G35460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 2
------ggttttatttgattatgtcacaagctt--ctgtttatgttgtaccttaattagtattacttttagatt-atattcccttctaagttatgtccttctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCTGAGCAG
| |||| | | || | | | | | | |||| | || || || | | ||| || || ||| ||| | | || | || || ||||||| | | |||||| ||||| ||||| ||||| || |||||||||||| ||||||||| ||||||| |||||||||||||||||
gtacttgattttttcctttgatctaaaacccataacggtttcctcgaattcgtagttcataatccacttatcttgatgttcactttttacttcaatattt---atgtagCTCAAGTTCCAGGAACTACTCAGGATCATCTACAGATATTTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 2
-ggttttatttgattatgtcacaagcttc--tgtttatgttgtaccttaattagta-ttacttttagattatattcccttctaagttatgtccttctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCTGAGCAG
| | || | || | | | ||| ||| || | | | |||| || | ||| ||| ||| || | || | | || | | ||||||| | | |||||| ||||| ||||| ||||| || |||||||||||| || |||||| |||| || |||||||||||||||||
tagaaattttggtttgtactggatgtttccttgtataagctattacttatttcttccttaatttgttgttaactttttcttaaattcgtatcgt----atatagCTCAAGTTCCAGGAACTACTCAGGATCATCTACAGATATTTAACATTGAAGCAAAGGCAAAGTTGAAGTCACATCAGATGCCTGAGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 2
ggttttatttgattatgtcacaagcttctgtttatgttgtaccttaattagtattacttttagat-tatattcc--cttctaagttatgtccttctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCTGAGCAG
| | |||| | | ||| | || ||||| | || | |||| |||| || || ||| || | |||| | |||| ||||||||||||| | ||||| || || |||||| | ||||| ||||| ||||| |||||||| || |||||||| ||||| ||||||||||||
attgtcatttagtagtttcattggtg---gtctatgtgtcaatttcaaagttatttgtttttcatatactttctggctcatgagtttaaacattcttttgaagCTCAACTTCCGGGAACCACCCAGGATCACTTGCAAATATTTAATATTGAGATGAAAGCCAAAATGAAATCATATCAAATGCCTGAGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 2
ggttttatttgattatgtcacaagcttctgtttatgttgtaccttaattagtattacttttagattatattcccttctaa-gttatgtccttctcttgaagCTCAACTCCAA-----GGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCTGAGCAG
| | | |||| || || | | | || || | | ||| || | | | || | |||| ||| | ||| | | ||| | | | || |||| |||||||| || |||||||| ||||| ||| ||||||| ||||||||||| ||||| ||||| || |||
----taacagcgtcctgtc-caccctcacatatgt-ttctatcgtcatttaattttcgactgaagagtacgtagtactaacgttgcgccctgtccgcgtgaatcagCCCTGATACCTGGTTCAACACAAGATCATCTCCAAATTTTCAACATCGAATTGAAAGCCAAGATGAAATCGTATCAAATGCCAGAACAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 2
-----ggttttatttgattatgtcacaagcttctgtttatgttgtaccttaattagtattacttttagatta-tattcccttctaagttatgtccttctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCTGAGCAG
| | || | | | | ||||| | || | || | | | || | || | || ||| |||||| | ||| | | || | || ||||| || || ||||| |||||||| ||| | ||||| ||||||||||| ||||| ||||| ||||||
aatatattctagttcagcctttgtatatgattctggctttggatgatgttgaatcacgaaatcttagtactaatgtttgtgtcttgtttatgtgaacc------agCCTTGATACCTGGTTCGACACAAGACCATCTCCAAATCTTTAACATCGAATTAAAAGCTAAGATGAAATCGTATCAAATGCCAGAGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 2
ggttttatttgattatgtcacaagcttctgtttatgttgtaccttaatta-gtattacttttagattatattcccttctaagttatgtccttctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCTGAGCAG
| | | | | || | | | || || | || | | | || | ||||||| | | || || | || ||||| || || ||||||||||| |||||||| || |||||||||||| |||| ||| | || |||
---------------------------------gtatgacatttcattttcgcgtgatccggaggatacaa------cttaactggtttgctcgtacgcagCTCAAATTCCTGGCACGAGCCAGGATCATCTCCAGATTTTTAACATAGAAATGAAGGCTAAGATGAAATCTCATCAAATGTCGGAACAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 2
ggttttatttgattatgtcacaagcttctgtttatgttgtaccttaat-tagtattacttttagattatattcccttctaagttatgtccttctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCTGAGCAG
| | | | | | | | | | || || | || | | | || | ||||||| | | || || | || ||||| || || ||||||||||| |||||||| || |||||||||||| |||| ||| | || |||
---------------------------------gtatgacatttcattctcgcgtgatccggaggatacaa------cttaactggtttgctcgtacgcagCTCAAATTCCTGGCACGAGCCAGGATCATCTCCAGATTTTTAACATAGAAATGAAGGCTAAGATGAAATCTCATCAAATGTCGGAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattagtattacttttagattatattcccttctaagttatgtccttctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCTGAGCAG
ccttaat putative branch site (score: 4)
ttatgtccttctctt putative PPT
tattacttttagatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggttttatttgattatgtcacaagcttctgtttatgttgtaccttaattagtattacttttagattatattcccttctaagttatgtccttctcttgaagCTCAACTCCAAGGAACAACTCAAGATCACCTACAAATTTTTAACATTGAAATGAAAGCAAAGATGAAATCTTATCAGATGCCTGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - cacaagc
- - - - - - - - - - - - -ttctgtt
- - - - - - - - - - - - - - - - - tgttgta