Sequence
atgc intronic sequence ATGC exonic sequence...ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
Basic information
species | Glycine max |
transcript | GLYMA02G35400.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 3
----ccatatgggatctaaataaacagttgttctgagttttta-cttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
| || | || | |||| | ||||| | | ||| || || || ||| || ||||||| | |||||||||||||||||||||| |||||||| ||||||||||||||||||| || || | || ||||| || ||||| || || || | | ||| ||||
taagcatcgtgatggcgttatgagaagttaaattatgttttaagtcttataccagaaatttct-----ctttattgattcttaacaagataaactctacttgcagTGACATGGAATGTGACCTGCACATACTCACAATTTCTTGCTCAGAAGACTCCAACCTGTTGTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
-ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgac-cttaacattgctctgatttatt-gcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
|||| || || | ||| | | | || | | | ||| | ||| | ||| | |||| ||||||| | || | || |||||||||||||||||||| |||||||| || |||||||||||||||| || || |||||||| || |||||||| || ||| | | ||| ||||
atcatagtggctccatatagaagttaaatttg--tcaaaatcttatacca-taaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
||| || || |||| ||| || || ||| | |||| | | || || ||| |||||||||| ||||||||||||||||||||||| || ||| ||||||| ||| | || | ||| ||||| || || ||||| || || | | ||| | ||
---------------gtaagtcatttcagtgttttttgtctttctggcgtcacaat------------tatgac---accctttcttcctttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g41310.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttat----tgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
|| || || | || | ||| || | || | | || | | || || | | |||||| | ||||||||||||||||||||| |||||||||||||| || | || || ||| | || | ||||| || |||||||| ||||| || | |||| | ||
gtaagatttttttctgaagtttccatgatcttagtatttgccgtgcaaagtagttcagggatgagctta-caatctattgcaacagattcagaattgttcttgtttcgatactgccttttcgtgcatcatcggtgaccgcttgatttcttttgtgcagTGACATGGAATGTGACTTGCACATATTCACAGATTGTCGCGCAAAGATCTCCGACGTGCTGCGTTTCGCTCTCGTCTTTTTACAATGATACCATAGTTAA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g35460.1 (Oryza sativa), 3'ss of exon 3
ccatatgggatctaaataaacagttgttctgagtttt----tacttcctactagcaaaatccatcaacttagtttgac--cttaacattgctctgattt---attgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
|| | | ||||| |||||| | || | | | | || | |||| || ||||||| || | | |||||||||||||||||| |||||||| || ||||||||||| || | || |||||||| || ||||| || ||| | | | | | |||
---------ataggacttgttgtttgttttgagttctatagtagaaaaaattcctatattcagtactactagtagtacttcttaacaaaaaggaaatctctattcacagTGACATGGAATGTGATCTGCACATACTCCCAATTTCTTGCACAAAAGGTTCCATCCTGCTGTGTTTCTCTCTCGTCGTTCGACAATGACAAAACTGTTGA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G009154_T01 (Zea mays), 3'ss of exon 2
------ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
|| | ||| | ||| | | |||| || | | | || | | | | | |||| || | | || ||||||||||||||||||||| ||||||||||| |||||||||||||||| || | |||||||| || |||||||| || ||| | | ||| ||||
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagttttgt-----ctatattttatagcattgagagttcttatcag-acattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCTGTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
------ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
|| | ||| | ||| | | |||| ||| | | | || | | | | ||||||| | | || ||||||||||||||||||||| ||||||||||| |||||||||||||||| || || |||||||| || |||||||| || ||| | | ||| ||||
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgt-----ctatattttatagcactgagggttcttaacag-acattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
----ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttat-tgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
| | || | || | | | |||| |||| |||| || | | || | ||||||| | | ||||| ||||||||||||||||||||| ||||||||||| |||||||||||||||| || || |||||||| || ||
ctaatcgcagatagtcctaggaagaattccatacaagttgc-acttttgtctag----attttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 3
----ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttat-tgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
| | || | || | | | |||| |||| |||| || | | || | ||||||| | | ||||| ||||||||||||||||||||| ||||||||||| |||||||||||||||| || || |||||||| || || ||||| || ||| | | ||| ||||
ctaatcgcagatagtcctaggaagaattccatacaagttgc-acttttgtctag----attttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAA
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 3
----ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
| | | | | || | | | || ||| ||| | | | | | | | | || | | || | | ||| ||| |||||||| |||||||| || ||||| ||||||||||| || ||||||| || || | || |||||||| | ||||| |||||| | || || | ||| |
aggatggcaagacacattgacaa-tggataatttgtgttcttaatatgcatttaaagagttctcaagatttaactaatctaa---tcttcctgtcctatggcagTGACTTGGAATGTTACTTGCACGTATTCACAATTCCTGGCTCAGAAGACGCCTACATGTTGTGTCTCATTGTCATCGTTCTATAATAACACTATAGTATC
upper sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
ccatatgggatctaaataaacagttgttctgagtttttacttcctactag---caaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
| ||| | | || || || | | | | | | | | | |||| || || || | ||| || | | | | |||||||||||||||| |||||||| ||||||||||| || |||||| ||| |||| ||||||||||||||||||||||||||| | | ||| |||||||
-agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgta--ctgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
tgatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC
ccatatg
- - - - - - -aaataaa
- - - - - - - - - - - - - - ctgagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctctg