Sequence
atgc intronic sequence ATGC exonic sequencegtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
Basic information
species | Glycine max |
transcript | GLYMA07G30990.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 6
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
| | | | || | | | ||||| || | | || | || || || | || || || ||||||||||| ||||| |||||||||||||||||||| | ||||||||||| |||||||||||||| | |||||||| | || ||||| ||| || |
-----------------------------------------gtaagttctacaattg-ttgttaataggttgtaattaatgtagtttaat-tgatgatcaaatacctcttttttcttttagATTCTTGGCAGTGGAATGTCAAATAAGATGTGGGAAAGCCTTGTTGAGCATGCAAAGACTTGTGTCTTAAGTGGAAAGCACTATGTATATTATGCTATTG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
|| | | || | | ||| ||| || | || | | | | | | | | | ||| | | | |||| ||||| ||||| ||||| ||||||||||||||||||||||| || || |||||||||||||| | ||||||||| |||| |||| ||| | || |
-------------------------------------gtaagattatttcctattcagcatttttcttctttttttc-------ttttgtttgagt-tctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 6
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
|| | | ||| | | | | ||| | ||| | | | | ||| || | | || | || || | |||| || |||||||||| ||| ||||||||||||||||||||| | |||||||||||| || ||||| |||||| | ||||| |||| || |||| || | |
------------------------gtaag-tcttattattcctctttgtaac-ttatattaagaattttgtttctttaaaactaaaatttggttttcttcttctgatattttc------agATTCTTGGCAGTAACATGTCAAATAAGATGTGGGAAAGTCTTGTTGAGCATGCGAAGACATGTGTTTTGAGTGGCAAACACTATATATATTACTCAAGCG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 6
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
| || ||| | || | | |||| | | || || ||| | | | || | | | | || ||||| || |||||||| || ||||| |||||||||||||||||||| | ||||||||||| |||||||| ||||| | |||||||| | ||| ||||||||| || ||
--------------------------gtaagttctatgatacctgtttt--tgcttactatattgtgatttatggtattccctatatggtttgacagccct-tg-----ttctttttatagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGAGCATGCAAAGACATGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
| | ||| | | | || || ||| | | | || || | | | | | || ||||||||||| || ||||| |||||||||||||||||||| | |||||||| || |||||||| ||||| | |||||||| | ||| ||||||||| || ||
-----------------------------------------gtaagttctatgat-accttattgtgatttatggtatttcctatatgatttgacacccct-----tgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
lower sequence: AC202073.4_FGT001 (Zea mays), 3'ss of exon 5
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
|| ||||| || | | | || | | | || | || | | |||| | | || ||| | | | | ||| |||| || |||||||||| ||| ||||||||||| ||||||||| | |||| ||||||| |||||||| |||||| | ||||| || | ||| |||| || | |
------------------gtaagtttagcatctctactttaactatgtt--tcatccacctctgtagtcttgtgaccaataccattttattt--cttctctctggttactc-----tgcagATTCTTGGCAGTAACATGTCAAATAGGATGTGGGAAAGTCTTATTGAGCATGCAAAGACATGTGTTTTGAGTGGCAACCATTATATATATTACTCAAGTG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 7
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggttt--gtatttgaatcgatgatatataattattttatggatacttc---ttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
| |||| || || || | ||| | ||||||||| | | ||||| || | | | || || |||||||||||||| ||||||||||||||||||||||||||| ||||||| ||||| ||||| ||||||||||| ||||| |||||||| || ||||||||||| |
--------------------------------------------gtaagaatgtacattttgttgtcatttcagaatttgaatccgtctattgtaatttttatttatttgtctccaattgttgtagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATGTTCTTGTGGAGCATGCAAAAACTTGTGTTCTAAGTGGGAAACTTTATGTTTACTATCCTGATG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
|| | | ||| || ||| | | | | | | | ||| | | | |||||||||| |||||||||||||||||||||||||| || ||||| || || || || || ||||| ||||| || || || || ||| | || |
------------------------------------------------------gtaagtaatgaaagttagttttttctttctctctctctg-tcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ05811 (Selaginella moellendorffii), 3'ss of exon 5
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
| | | | || ||| | | | | | || | | | | | ||| | | | |||||||||| |||||||||||||||||||||||||| || ||||| || || || || || ||||| ||||| || || || || ||| | || |
----------------------------------------------gtaagtaatgagtttttttctctctctttctctctctttctt------tcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
cttcttatt CT-rich tract
atgatatataattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG