Sequence
atgc intronic sequence ATGC exonic sequencegtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
Basic information
species | Glycine max |
transcript | GLYMA08G06320.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 6
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactata-cttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
| || | ||||| || | | || | | |||| ||| || | | || || ||| || || ||||||||||| || || |||||||||||||||||||| | |||||||||||||||||||||||||| | |||||||| | |||||||| ||| || ||
-------------------------------------------------------------------gtaagttctacaattgttgttaataggttgtaattaatgtagtttaattgat--gatcaaatacctcttttttcttttagATTCTTGGCAGTGGAATGTCAAATAAGATGTGGGAAAGCCTTGTTGAGCATGCAAAGACTTGTGTCTTAAGTGGAAAGCACTATGTATATTATGCTATTG
upper sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatac-ttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
||| ||| || | ||| || | | | | | | | | | ||| | | | |||| ||||| || || ||||| ||||||||||||||||||||||| || ||||||||||||||||| | ||||||||| ||| |||| ||| | || |
-----------------------------------------------------------------------gtaagattatttcctattcagcatttttcttctttttttcttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
upper sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 6
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
|| |||| || | || || | || | || || ||| | | ||| |||||||| || | | || |||||||||| || ||||||||||||||||||||| | ||||||||||||||| ||||| |||||| | ||||| |||| ||| |||| || | |
------------------------------------------------------gtaagtcttattattcctctttgtaacttatattaagaattttgtttct---ttaaaactaaaatttggttttcttcttctgatattttcagATTCTTGGCAGTAACATGTCAAATAAGATGTGGGAAAGTCTTGTTGAGCATGCGAAGACATGTGTTTTGAGTGGCAAACACTATATATATTACTCAAGCG
upper sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 6
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaat-tgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
| | |||| | | ||| |||| | || ||| | |||| ||| | | | ||| | | | | ||| || || |||||||| || || || |||||||||||||||||||| | |||||||||||||||||||| ||||| | |||||||| | ||||||||||||| || |
-----------------------------------------------------gtaagttctatgatacctgtttttgcttactatattgtgat-ttatggtattccctatatggttt-----gacagcccttgttcttt-ttatagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGAGCATGCAAAGACATGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
upper sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
| | || ||| | | || || | |||| ||| | | | ||||| | | | | ||| || ||||||||||| || || || |||||||||||||||||||| | |||||||| ||||||||||| ||||| | |||||||| | ||||||||||||| || |
----------------------------------------------------------------gtaagttctatgataccttattgtg---atttatggtatttcctatatgattt-----gacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
upper sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
lower sequence: AC202073.4_FGT001 (Zea mays), 3'ss of exon 5
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
| | || ||| || | | | ||| | |||| || | || || ||||||| || || | || || || |||||||||| || ||||||||||| ||||||||| | |||| |||||||||||||||| |||||| | ||||| || | |||| |||| || | ||
---------------------------------------------gtaagtttagcatctctactttaactatgtttcatccacctctgtagtcttgtgaccaataccat----tttatttc-ttctctctggttactc--tgcagATTCTTGGCAGTAACATGTCAAATAGGATGTGGGAAAGTCTTATTGAGCATGCAAAGACATGTGTTTTGAGTGGCAACCATTATATATATTACTCAAGTG
upper sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 7
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
| || | |||| ||| | | ||| || || ||| | | | ||| ||| | | || |||||||||||||| || |||||||||||||||||||||||| ||||||| ||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||
-------------------------------------------------------------gtaagaatgtacattttg-ttgtcatttcagaat--ttgaatccgtctattgtaatttttatttatttgtctccaattgttgtagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATGTTCTTGTGGAGCATGCAAAAACTTGTGTTCTAAGTGGGAAACTTTATGTTTACTATCCTGATG
upper sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
| | ||| || | |||| | | || | | | | | | || | | | |||||||||| || ||||||||||||||||||||||| || |||||||| || || || || ||||| ||||| || ||||| || ||| | || |
-------------------------------------------------------------------------------gtaagtaatgaaagttagttttttctttctctctctctgtcagctcatgta-gttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
upper sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ05811 (Selaginella moellendorffii), 3'ss of exon 5
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
|| | |||| || || | | | || || | | | | | | |||||||||| || ||||||||||||||||||||||| || |||||||| || || || || ||||| ||||| || ||||| || ||| | || |
----------------------------------------------------------------------------gtaagtaatga-gtttttttctctctctttctctctctttctttcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
ggttaac putative branch site (score: 3)
cttccttatt putative PPT
attttatatgtcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA