Sequence
atgc intronic sequence ATGC exonic sequencegtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
Basic information
species | Glycine max |
transcript | GLYMA04G09080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
|| | | || | ||| | | || | | ||| | || ||| |||| | ||| ||| || || ||| |||| || |||||||||| ||| ||| ||||||||| |||||||||||| |||| ||||||||||| ||||||||
gtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagttgcatttat----attcacgcttttctttatac----cagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G342407_T01 (Zea mays), 3'ss of exon 4
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
| | | ||| | | | | | |||||| || || || || | | || | ||| |||||||| || || ||||| |||||| ||| ||| ||||| ||||||||||| ||||||||||||||||||||||| ||
------------------gtttgtcacttacacattttatgaatttgatggattttttccttacataaatccattaaatggta-attttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G355274_T01 (Zea mays), 3'ss of exon 3
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
| | | ||| | | | | | |||||| || | || || | | || | ||| ||||||| || || ||||| |||||| ||| ||| ||||| ||||||||||| ||||||||||||||||||||||| ||
------------------gtttgtcacttacacattttatgaatttgatggatttgttccttacataaatccattaaatggta-attttttgtagGACGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattg--atgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
|| || || | | | | ||| |||| || ||| | | | | | || |||| || | || || ||||| || | |||||||| ||| ||| ||||||||| ||||| ||||| |||| ||||||||||| ||||||||
-------------gtctttatgccttctctggaatt---tttaattgtaattcatcgtagctgcattagcataaacgtttt----ttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
||||| |||| | || | | ||| || | | |||| || || | ||| ||| |||| || | | |||||||| || || || ||||||||||||| ||||||||| || || ||||| || || ||||||||||| ||||||||
gtatgctgtttgtgtttgcaagtttactt---gctttcttttggttttctgtgatctgtaatgtgatt-ttgatgtgtccactt-----ttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------gtatggtgttagcgtgttg-atatttggttaaagagtgtgtttgattgatgcatat--------tggatttgtcattattgac---gtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
|| ||| | ||| || ||| | | | |||| || || | ||| || | || | || || || ||| | | || | | ||||||| ||||| ||||| ||| | |||||||| || ||||||||||| ||||| || |||||||| ||||||||
gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgagtatctttgctttgtgtctggaagtacaaactgagtcttgttttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------gtatggtgttagcgtgtt-----gatatttggttaa--agagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
| | | ||| |||| |||| | | | | | | | |||| || || | | || | | ||||| || | || |||| || || || || |||||| | || || || || ||||||||||| ||||| |||||||||||||||||||
gtattcaatttcttacaatttgttctgctctacttctttcgcagcagcatgtttggaagatactctgcatattgcatcgaggtcttgtgatttttaatgtaataagttttgtattcatattgaactcgtttgtgcagGTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 2
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
| | |||| | | ||| | || | || || |||| ||| | |||| || | || || |||||||| ||||||||||| ||||| || || ||||| || || |||||||||||| |
-----------------------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttg--cgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
|| ||| | | || | ||| ||||| | | | | | | | || || | |||| || || || ||||| || |||||||| ||||| ||||| ||||| ||||| ||||||||||| |||||||
-------------------gtagactgttcgaagatttgctcagttgg-----attggctcttttctcagcggctgatcaaa--gatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
| | |||| | | ||| | || | || || |||| ||| | |||| || | || || |||||||| ||||||||||| ||||| ||||| ||||| || || |||||||||||| |
-----------------------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttg--cgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctat--tgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
||| ||| | | ||||||| || || | | || || | || | |||| || || || ||||| || |||||||| ||||| ||||| ||||| ||||| ||||||||||| |||||||
-----------------------------gtagactgttcgaagattttctcagttggattgctcttttctcagcggctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
ctctatt CT-rich tract
tcattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG