Sequence
atgc intronic sequence ATGC exonic sequence...attaatgtgaaagcactgatttcaggctagctatgctttttttttccctttcttatttactaatgccttgtattgatgtttccattctactatgactcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
Basic information
| species | Glycine max |
| transcript | GLYMA20G01240.1 |
| intron # | 6 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------attaatg-----tgaaagcactgatttcaggctagctatgctttttttttccctttcttatttactaatgccttgtattgatgtttccattctactatgactcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
||| || | | | || |||| | | || || || | | ||| | | | ||| | | ||| || | || ||||||| ||||||||||| ||||| || ||| | || || ||| |||| |||||||||||||||||||||||||| || ||||| |||||| |||||||||
gtactcatatatttgaatttacatgcttgcgtcctgaatatggtgtcatggtgtctcagtctggtatattgatacatcatacatgtaccattttct--ccacttaagcaattgtactttcttcgcgaggcatcagtgcgat-tgctgactaaatatttgtttctcaacaaagATTGCTGATGTGTGGTCGTGTGGAGTAACCCTCTACGTAATGCTGGTTGGTGCATATCCTTTTGAGGATCCAGATGAGCCTAAGAATTTCAGGAAGACAA
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 6
-attaatgtgaaagcactgatttcaggctagctatgctttttttttccctttcttattt-actaatgccttgtattgatgtttccattctactatgactcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
| | | | | || | | | | || || | | | | || || || |||| | || |||| || ||| ||| ||||| ||||| ||||| ||||| ||||||| ||| | || |||||||||||||| ||||||||||| || ||||| || ||||| || ||||
tgtcccttctttttctttaaaacagaagtatttccattactgataaccgcttagtgtaggaatcctggctcatactgatacattatttatactgaaac--agACTGCTGATGTATGGTCCTGTGGTGTGACTCTATATGTTATGGTAGTTGGTGCATATCCTTTCGAGGATCCAGAAGAGCCTAAGAACTTCCGTAAAACAA
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G066867_T01 (Zea mays), 3'ss of exon 5
attaatgtgaaagcactgatttcaggctagc-tatgctttttttttccctttcttattta-ctaatgccttgtattgat----gtttccattctactatgactcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
| | |||| | || || | | |||| | || | || | | || | | | | || |||| | || | || ||||||||||| ||||| || || | || || ||| |||| ||||||||||| |||||||| ||||| || ||||| |||||| |||||||||
------atacacgcacggtttgtagtcatgtatatgtatagcaggaaactatgttggcaagttggaaccctatgtcagtcactaactcttcgttactgaaaacaagGTCGCTGATGTGTGGTCATGTGGAGTAACGCTGTACGTGATGCTGGTCGGTGCATATCCATTTGAGGACCCAGATGAGCCTAAGAATTTCAGGAAGACAA
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 6
attaatgtgaaagcactgatttcaggctagctat--gctttttttttccctttcttatttactaa--tgccttgtattgatgtttccattctactatgactcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
|| | | | ||||||| | ||| || | || ||| ||| || | | | ||||| | || || | | |||||||| ||||| ||||| ||||| || ||| | ||||| ||| || ||||||||||||||||| || ||||| || ||||| || ||||| |||||||
--aaacctcatatttatgatttctattttagtattaactgcctggttacctcctttacgaggaaagcttctcctcactgatgaatttgtt-tatgacaaa-cagATTGCTGATGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGCTGTTGGTGCATATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAA
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 7
attaatgtgaaagcactgatttcaggctagctatgctttttttttccctttcttatttactaatgccttgt----attgatgtttccattctactatgactcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
|| | | ||||||| | | | | | | | || ||| | | ||| | | |||| | || ||| | | |||||||| || || ||||| ||||| || ||| | ||||| ||| | || || |||||||||||||| |||||||| || ||||| || ||||| |||||||
---aaacttccacttatgatttctcttttagtgttcactgtctggttacctcctatatgaggaaagcttctcctcaccgatggatttgtt-tacgacaaaacagATTGCTGACGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGTTGTTGGCGCATATCCTTTTGAAGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAA
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
---------attaatgtgaaagcactgattt-caggctagctatgctttttttttccctttcttatttactaatgccttgtattgatgtttccattctactatgactcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
| | | || ||||||| | || || ||| |||| | ||| | | ||||| | || || | || || | |||| |||||||||| |||||||||||||| || | ||||||||| |||| || ||||||||||| || ||||| |||||||| || |||||| |||| || |
ttggtgaagaaagctattaagagtctgatttgtaaactgataattcttgagttttggttgaattagtca--aatgcatcctaatgttcttcttttttt--------tcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 6
--attaatgtgaaagcactgatttcaggctagctatgctttttttttccctttcttatttactaatgccttgtattgatgtttccattctactatgact-cagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
||||| ||| | | |||| || | ||||||||| |||| || | ||| | | | |||||||||||||| |||||||||||||| ||||||||||| ||| |||||||||| || || |||||||| || ||||||||||| || |||| |||||||
tggaaaatgtagtttgtatgagtataatggttatatgagaacaccaaaatatttagacttactaatgttttgttgctctgat---atttgatcacattttcagATTGCAGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAA
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------attaatgtgaaagc-actgatttcaggcta--gctatgctttttttttccctttcttatttactaatgccttgtattgatgtttccattctact-atgactc--agATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
||| || | | | || |||| || |||||| | | | || | | || | | | ||| | | | | || || ||| || ||||||| ||||||||||| ||||| |||||||| || || ||||| ||||| |||||||| ||||||||||| || || || | |||||| |||| || |
gtatgctgctcagacgaggattcgtttttgtgaggtgattggatttctggtatctctgcggagctcagtgtactatcgaaattttttagggcatgtggcatcaagttat-cagggaactgagatatgcctacttcttgtgaatcgcagATTGCCGATGTGTGGTCGTGTGGAGTGACCTTGTACGTGATGTTAGTGGGGGCATATCCGTTTGAGGATCCCGATGACCCAAGGAATTTCAGGAAAACCA
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------attaatgt---gaaagcactgatttcaggct-agctatgctttttttttccctttcttat-ttactaatgc-------cttgt--attgatgtttccattctactatgact--cagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
||| | || | || | ||| || | || | ||||| | | | |||| | ||| |||| | | | | | | | ||| ||||||||||||||||||||||| || || ||||| || || |||||||| || ||||||||||| |||||||| || || || | |||||| |||| || |
gtaagtttttcggaagcgtgttggttttagtggaataaattggttcttggacaatgctattatcatgcggaactgaagctatttttggtgtcggtgaggttacaagtgcacggctctttgtcagctaaagaggctgatttgccgtgatatacagATTGCAGATGTGTGGTCTTGCGGTGTTACCTTGTACGTGATGTTGGTTGGAGCATATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCA
upper sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------attaatgtgaaagcactgatttcaggctagctatgctttttttttccct--------ttcttatttactaatg---------ccttgt------attgatgtttccattctactatga--ctcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
|| | || | | || | | ||| ||| | | | || | |||||||| | |||| | | ||| | || | || || |||||||| ||||||||||| || || |||||||| || |||||||||||||| ||||| || || |||||||| | || || | |||||| |||| || |
gtacgtggtttgcacaagggtttttgaccgcaaggattggggtttcgcttcatgatgtctttctactgaatcaagtgtgttagtgtttactaaagttcaaggcaccttatcggggaactgaaggaacccacttgcttcgagatgcagATTGCGGATGTGTGGTCGTGCGGTGTGACCTTGTACGTCATGTTGGTGGGAGCATACCCATTCGAGGATCCCTATGACCCAAGGAATTTCAGGAAAACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctttcttatttactaatgccttgtattgatgtttccattctactatgactcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
ttctact CT-rich tract
tcttatttactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attaatgtgaaagcactgatttcaggctagctatgctttttttttccctttcttatttactaatgccttgtattgatgtttccattctactatgactcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattct
