Sequence
atgc intronic sequence ATGC exonic sequence...gtagtagaatgaaaggttgtgattactgttatgcatgcatggtctagaattcagctagctttttatctgttgctaatgtttacactcaattatgactcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
Basic information
species | Glycine max |
transcript | GLYMA02G15330.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------gtagtagaatgaaaggttgtg-at-tactgttatgcatgcatggtcta--gaattcagctagctttttatc--tgttgctaatgttta--cactcaattat-gactcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
| ||| | ||| | | | || ||| || | | | | | | | | | || ||| || | || || | | || | || |||| || ||||||||||| ||||| || ||| | || || ||| ||||||||||||||||||||||||||||||| || ||||| |||||| | |||||||
gtactcatatatttgaatttacatgcttgcgtcctgaatatggtgtcatggtgtctcagtctggtatattgatacatcatacatgtaccattttctccacttaagcaattgtactttcttcgcgaggcatcagtgcgattgctgactaaatatttgtttctcaacaaagATTGCTGATGTGTGGTCGTGTGGAGTAACCCTCTACGTAATGCTGGTTGGTGCATATCCTTTTGAGGATCCAGATGAGCCTAAGAATTTCAGGAAGACAA
upper sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 6
-------------gtagtagaatgaaag-gttgtgattactgttatgcatgcatggtctagaattcagctagctttttatctgttgctaatgtttacactcaattatgactcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
|| || ||| || ||||||| || | || | || ||| | || || ||| | ||| | | | | |||| ||| || |||| || ||||| ||||| ||||| ||||| ||||||| ||| | ||||||||||||||||| ||||||||||| || ||||| || ||||| || ||||
tgtcccttctttttctttaaaacagaagtatttccattactgataacc--gcttagtgtaggaatc--ctggctcata--ctgatac-attatttatactgaaa-------cagACTGCTGATGTATGGTCCTGTGGTGTGACTCTATATGTTATGGTAGTTGGTGCATATCCTTTCGAGGATCCAGAAGAGCCTAAGAACTTCCGTAAAACAA
upper sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 7
gtagtagaatgaaaggttgtgattactgttat-gcatgcatggtctag--aattcagctagctttttatctgttgctaatgtttacactcaattatgac---tcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
|| || ||||| || || | | | || |||| | | || || | || | || | | | | ||| ||| ||||| || || || ||||| ||||| || ||| | ||||| ||| | ||||| |||||||||||||| |||||||| || ||||| || |||||||||||||
------aaacttccacttatgatttctcttttagtgttcactgtctggttacctcctatatgaggaaagcttctcctcaccgatggatttgtttacgacaaaacagATTGCTGACGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGTTGTTGGCGCATATCCTTTTGAAGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAA
upper sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 6
gtagtagaatgaaaggttgtgattactgttat-gcatgcatggtctag--aattcagctagctttttatctgttgctaatgtttacactcaattatgac--tcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
| | | || ||||| || || | | || | | || | | || || | || | || | | | | ||||||| ||||| || ||||| ||||| ||||| || ||| | ||||| ||| |||||||||||||||||||| || ||||| || ||||| || |||||||||||||
-----aaacctcatatttatgatttctattttagtattaactgcctggttacctcctttacgaggaaagcttctcctcactgatgaatttgtttatgacaaacagATTGCTGATGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGCTGTTGGTGCATATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAA
upper sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G066867_T01 (Zea mays), 3'ss of exon 5
gtagtagaatgaaaggttgtgattactgttatgcatgcatggtctagaattcagctagctttttatctgttgctaatgtttacactcaattat---gactcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
|| | | | |||| | | |||| || || | | || || | || | | | || || ||| | || | || ||||||||||| ||||| || || | || || ||| |||| ||||||||||| |||||||| ||||| || ||||| |||||| | |||||||
---atacacgcacggtttgtagtcatgtatatgtatagcaggaaactatgttggcaagttggaaccctatgtcagtcactaactcttcgttactgaaaacaagGTCGCTGATGTGTGGTCATGTGGAGTAACGCTGTACGTGATGCTGGTCGGTGCATATCCATTTGAGGACCCAGATGAGCCTAAGAATTTCAGGAAGACAA
upper sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
gtagtagaatgaaaggttgtgattactgttatgcatgc--atggt-ctagaattcagctagcttt--ttatctgt-tgctaatgtttacactcaattatgactcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
| || | | || || | ||| | || | | || | || || || | | | || | | || | |||||||| | || |||| | |||||||| |||||||||||||| || | ||||||||| ||||||| ||||||||||| || ||||| |||||||| || |||||| | || || |
ttggtgaagaaagctattaagagt-ctgatttgtaaactgataattcttgagttttggttgaattagtcaaatgcatcctaatgttcttcttttttt-----tcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
upper sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 6
gtagtagaatgaaaggt-tgtgattactgttat-gcatgcatggtctagaattcagctagctttttatctgttgctaatgtttacactcaattatgact-cagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
| | |||| | | | ||| || | | ||| | | ||| | | | || | ||| | | | | | | || | | ||||| |||||||| |||||||||||||| ||||||||||| ||| |||| ||||| || || |||||||| || ||||||||||| || |||| ||||||||
--tggaaaatgtagtttgtatgagtataatggttatatgagaacaccaaaatatttagacttactaatgttttgttgct-ctgatatttgatcacattttcagATTGCAGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAA
upper sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------gtagtagaatgaaaggttgtgattactgttatgcatgcatggtctagaattcagct--agcttttta---tctgttgc-taatgtttaca-----ctcaattatgact---------------cagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
| ||| | | |||| ||| ||| ||| | || | | | |||||| ||| || | | ||| || || | |||| || ||||| || ||||||||||| ||||| |||||||| || || ||||| || || |||||||| ||||||||||| || || || | |||||| | || || |
gtatgctgctcagacgaggattcgtttttgtgaggtgattggatttctggtatctctgcggagctcagtgtactatcgaaattttttagggcatgtggcatcaagttatcagggaactgagatatgcctacttcttgtgaatcgcagATTGCCGATGTGTGGTCGTGTGGAGTGACCTTGTACGTGATGTTAGTGGGGGCATATCCGTTTGAGGATCCCGATGACCCAAGGAATTTCAGGAAAACCA
upper sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------------------gtagtagaatgaaaggttgtgattactgtta-tgcatgcatggtctagaattcagctagctttttatctgttgctaatgtttacactcaattatgactcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
|| || ||| || || | || || | ||| | | || ||| ||| || | | | | | | | | || | ||||| ||||||||||||||||| || || ||||| || || ||||||||||| ||||||||||| |||||||| || || || | |||||| | || || |
gtaagtttttcggaagcgtgttggttttagtggaataaattggttcttggacaatgctattatcatgcggaactgaagctatttttggtgtcggtgaggttacaagtgca--cggctctttgtcagctaaagaggctgatttgccgtgat-atacagATTGCAGATGTGTGGTCTTGCGGTGTTACCTTGTACGTGATGTTGGTTGGAGCATATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCA
upper sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------gtagtagaatgaaaggttgtgatta---ctgttatgcatgcatggtctagaattcagctagctttttatctgttgctaatgtttacactcaatt-atgactcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
| | |||| || | | | | || | | ||| | |||| | || | | || | |||| || || ||||| || ||||||||||| || || |||||||| || ||||||||||| || ||||| || || |||||||| | || || | |||||| | || || |
gtacgtggtttgcacaagggtttttgaccgcaaggattggggtttcgcttcatgatgtctttctactgaatcaagtgtgttagtgtttactaaagttcaaggcaccttatcggggaactgaaggaacccacttgcttcgagatgcagATTGCGGATGTGTGGTCGTGCGGTGTGACCTTGTACGTCATGTTGGTGGGAGCATACCCATTCGAGGATCCCTATGACCCAAGGAATTTCAGGAAAACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaattcagctagctttttatctgttgctaatgtttacactcaattatgactcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
tgctaat putative branch site (score: 2)
tttttatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtagaatgaaaggttgtgattactgttatgcatgcatggtctagaattcagctagctttttatctgttgctaatgtttacactcaattatgactcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - ggttgtg
- - - - - - - - - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactcaa