Sequence
atgc intronic sequence ATGC exonic sequencegtatggtgttagttagggtgttgattgatatttggttaaagagtgtgtttgactgatgcatattggatatgtcattggtacgtattgttctattgattgtagATAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCCCCACATGAGTGGCAGGTTTACAA
Basic information
species | Glycine max |
transcript | GLYMA04G09070.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
gtatggtgttagttagggtgttgattgatatttggttaaagagtgtgtttgactgatgcatattggatatgtcattggtacgtattgttctattgattgtagATAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCCCCACATGAGTGGCAGGTTTACAA
|| || | | | ||| | | || | | ||| | || |||| | | |||| || | || | || || || | || |||||||||| ||| ||| ||||||||| |||||||||||| | || |||||||||| ||||||||
-------gtcagctcttctaatc-cggatgtctttttcatttccatatttaaaatat-catagttg------catttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G342407_T01 (Zea mays), 3'ss of exon 4
gtatggtgttagttagggtgttgattgatatttggttaaagagtgtgtttgactgatgcatattggatatgtcattggtacgtattgttctattgattgtagATAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCCCCACATGAGTGGCAGGTTTACAA
| ||| | || | || ||||| ||| | | || || | | ||| |||||| | || || ||||| |||||| ||| ||| ||||| ||||||||||| || ||| |||||||||||||||| ||
----------------------gtttgtcacttacacattttatgaatttgatggattttttccttacataaatccattaaatggta----attttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G355274_T01 (Zea mays), 3'ss of exon 3
gtatggtgttagttagggtgttgattgatatttggttaaagagtgtgtttgactgatgcatattggatatgtcattggtacgtattgttctattgattgtagATAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCCCCACATGAGTGGCAGGTTTACAA
| ||| | || | || ||||| ||| | | || || | | ||| |||||| || || ||||| |||||| ||| ||| ||||| ||||||||||| || ||| |||||||||||||||| ||
----------------------gtttgtcacttacacattttatgaatttgatggatttgttccttacataaatccattaaatggta----attttttgtagGACGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
gtatggtgttagttagggtgttgattgatatttggttaaagagtgtgtttgactgatgcatattggatatgtcattggtacgtattgttctattgattgtagATAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCCCCACATGAGTGGCAGGTTTACAA
||||| |||| || | || || || ||| || | | || | | || || | |||| ||| | || | | |||||| | || || || ||||||||||||| ||||||||| || || ||||| || || |||||||||| ||||||||
gtatgctgtttgt--gtttgcaagtt--tacttgctt------tcttttggttttctgtg-atctgtaatgtgattttgatgtgtccactt-----ttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgactgatgcatattggatatgtcattggtacgtattgttctattgattgtagATAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCCCCACATGAGTGGCAGGTTTACAA
tattgat putative branch site (score: 3)
ttctatt CT-rich tract
tattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggtgttagttagggtgttgattgatatttggttaaagagtgtgtttgactgatgcatattggatatgtcattggtacgtattgttctattgattgtagATAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCCCCACATGAGTGGCAGGTTTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG