Sequence
atgc intronic sequence ATGC exonic sequence...caagcaactcatctttcacctggcaatgtgtaatgtgcgttatcttcccttattttggataaaagaattgatatcaggtaccattgattattctttgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG
Basic information
species | Glycine max |
transcript | GLYMA07G14800.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 5
-------------------caagcaactcatctttcacctggcaatgtgtaa----tgtgcgttatcttcccttattttggataaaagaattgatatcaggtaccattgattattct---ttgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG
| | || || | ||| || | | | | | | |||| || ||| | | ||| | ||| ||| || ||||||||||||||||| | ||||||||||| |||||||| ||||| ||||||||||| ||||||||| |
gttggtgcattaatttcaataggtttctatctgtttgctcattcatgataaaaatttatacagcaagcttaacttgcttgggccttgcttttagtatttgttcattcatgttacttcgaattgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG
upper sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 5
---------------------------caagcaactcatctttcacc-tggcaatgtgtaatgtgcg-ttatcttcccttattttggataaaagaattgatatcaggtaccattgattattctt-----tgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG
| | || |||| | ||| | || | | ||| ||| | | | | | || ||| | ||| | ||| || | ||| || ||| || ||||||||||||||||| | ||||||||||| |||||||| ||||| ||||||||||| ||||||||| |
gttggtgcattaatttcaatagatttttatctgtttgctcattcatgataaaaatttatacagcaagcttaacttgcttgggccttgcttttagtatttgt-tcattcatgattcatgttacttcgaactgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG
upper sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
-------------------caagcaactcatcttt-cacctggcaatgtgtaatgtgcgttatcttcccttattttggataaaagaattgatatcaggtaccattgattattctttgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG
|| | |||| || | || || | || | | | || || |||| || | | || | | | |||| | || | ||| || |||||||||||||| | | ||||||||||| |||||||| || || ||||||||||| |||||||||| |
gttggtacatttatttccctaatttattcatgttcactgcttacataatctagcttatgct-tccaagtgtaatttgcatgtagca--tgctcttaatattcattttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
upper sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 5
-caagcaactca---tctttcacctggcaatgtgtaatg--tgcgttatcttcccttattttggataaaagaattg-atatcaggtaccattgat-tattctttgc---------agACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG
| || ||| | | |||| | || | | | |||| | | || | || ||| || | | | ||||| | |||| ||| || ||||||| |||||| | | ||||||||||| |||||||| || || ||||| ||||| |||||||||| |
gttggtgccttgatttctctattttttttatgttcactgcttacatgatctatcatatacttccaagtgtgatttgtatgttgcatgctcttgatgttcactttatttcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG
upper sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------caagcaactc---atctttcacctg-gcaatgtgtaatgtgcgttatcttcccttatttt---ggataaaagaattgatatcaggtaccattgattattctttgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG
| | | | ||| || | || || |||| | | || |||| | ||| | ||| || | | |||| | || | | |||||||| ||||||| ||||| || ||| ||||||| ||||| || ||||| ||||||||||| ||||||||||||||||||
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgctt--ctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
upper sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
caagcaactcatctttcacctggcaatgtgtaatgtgcgttatctt--cccttattttggataaaagaattgatatcaggtaccattgattattctttgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG
| || || | || ||| | || | | | | | | || | | ||| | | || | | |||| | |||| | || ||||||||||| ||| |||| |||||||| || |||||||| || |||||||| ||||||||||||| |
--tatattatattatttaggaaataaattgtggtatgaagcaaatgagtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcccttattttggataaaagaattgatatcaggtaccattgattattctttgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG
cattgat putative branch site (score: 4)
ttattcttt CT-rich tract
ataaaagaattgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caagcaactcatctttcacctggcaatgtgtaatgtgcgttatcttcccttattttggataaaagaattgatatcaggtaccattgattattctttgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - caactca
- - - - - - - -tcacctg
- - - - - - - - - - - -caatgtg
- - - - - - - - - - - - - - - -aatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa