Sequence
atgc intronic sequence ATGC exonic sequence...atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
Basic information
species | Glycine max |
transcript | GLYMA14G33480.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttggga-atgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
||| | | | | ||| | | || || || | | ||| ||||||| || |||| |||| ||||||||||||||||||||||||||||| || || || ||| |||||||| ||||| || | ||||| || ||||| || || || | |
--------------gtaagcactaagc-accagcaacggcaacgccatccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g36480.1 (Oryza sativa), 3'ss of exon 3
atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataa---tgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
||| | | || | | || || | ||| | | || | || || | | || |||| |||||||||||||||||||||| |||||| || || | ||| |||||||||||||| || | ||||| || ||||| || || || | |
------------------gtaggtgcttcattccgtctccggccaaggcgacggcgatgtagacgacgatggcaaattcattcgatcggttgggtttttgcagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGGCCGCACAAGGGTGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGGA
upper sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G878558_T01 (Zea mays), 3'ss of exon 3
--------------------atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
|||| | || || || | | ||| | | | | ||| | | || || |||| | | | |||| ||||||||||||||||||||| ||||||| | || | | ||| |||||||| ||||| ||||| ||||| || ||||| | || || | |
gtgagttgccgctccatcgtgtttcccttcccgtggaaccatgcatgtcctcctctccacgactgtgttagcttaaatacacgcacgtgcgtc-tgttcct---------ctacgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGATCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCATGGTGTTCGAGCACCCGGCGCAGCCGGGCA
upper sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
-------------------------atttcaagggaccaaaaagt--attttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
|||| | | | || | ||| | || || || | | ||| | |||| ||| | ||| | | |||| ||||||||||||||||||||| ||||||| || | | ||| |||||||| ||||| ||| | ||||| || ||||| || || || | |
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtcc-gttcctgcgc--gcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G568636_T01 (Zea mays), 3'ss of exon 3
atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatg-tgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
| | ||| | | | | | | | | | || | || | | || || ||| | | ||| || ||| |||| |||||||||||||||||||||| |||||| || || | || |||||||| ||||| || | ||||| || ||||| || || || | |
----------gtacatatatatactagcacataatattaatactgaataagtttctgtttctgctcctg----atgatatataaatctgatgatggcacagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGTCCGCACAAGGGCGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGCA
upper sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatg------tgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
||| | |||| | | | || ||| | | || | | |||| ||| ||| || || | ||||||| || |||| ||||||||||||||||||||||| || ||||||||||| ||||| |||| ||| |||||||| || || || || || || || | |||| ||
---tcatagttgcaaacatgagaggcgtgcgtttatg---acgtgattttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
upper sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
---atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
| | | || | | | | | | | || | | || ||| | || | | ||| | | | | || |||| ||||||||||||||||||||| ||||||| || ||||| | | | | | || | | | || || ||||| || | || | |
agaactgctgcgggttccatgtcgtctac--gatgtattgcgct-gtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
upper sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
---atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
| || | || | || | || | | | | ||| ||| | || || || |||| | | || | | |||| ||||||||||||||||||||| ||||||| | | ||||| || | | | ||| | ||| || ||||| || || |||| |
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgctgttctga-atgtcctcgccgtggtgtgctac--agGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
upper sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ14822 (Selaginella moellendorffii), 3'ss of exon 4
atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
|| | | || | | | | || || | || || | | ||| | || || | |||| ||||||||||||||||||||| ||||||| | |||| | || | | | | | ||| || ||||| || | || || |
------------------gtgagtggaagtgaattctttggattga-------tcggtggttctcatggttcgatctctcggg----ctatggtg-gcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCGTCCCTGCAAGGGGAAGCTCGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGCCA
upper sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
atttcaagggaccaaaaagtattttcccgctttttttcacaagtaa--agcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
||| | | | | || | | | | | |||| ||| || || | | ||| | || || | |||| ||||||||||||||||||||| ||||||| || |||| | ||| | | | | | ||| || ||||| || | || | |
------------------gtaagtggcagtggatctttgggattgatcggtagttctgatggttcg---------atctctcggg----ctatggtg-gcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
ttctaat putative branch site (score: 2)
ttatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
- - - - - accaaaa
- - - - - - - - - - - - tcccgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca