Sequence
atgc intronic sequence ATGC exonic sequence...gacaagctctttcttggtgttccttaatcttgtgtgccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
Basic information
species | Glycine max |
transcript | GLYMA20G00320.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 5
gacaagctctttcttggtgttccttaatcttgtgtgccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgt-----acatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
| | ||| | || || | | ||| |||||| | || | | |||| ||| | | | || | | | || | ||||| |||||||||||||| ||||| || || ||||| || || |||||||| |||||| | ||||| ||||| |||| ||||| |||||||| || |
----tgttttttgaggtcatttttttaattgatgtcatttttaattataccatg-gtatatattgattatatgaatgaaggatgtcttctttttaatatatatagTGGTGAGAGTGGAGCAGGAAAGACAGAAACTGCAAAGATTGCTATGCAGTATTTGGCTTCTCTTGGAGGTGGGGGTGGCATAGAATATGAGATCCTACAA
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 5
gacaagctctttcttggtgtt-----ccttaatcttgtgt--gccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
|| || || | || | ||||| || | || || | | || ||| || | | | | | || || | || | || |||||| |||||||||||||| || || || || |||||||| || ||||||||| ||||| ||||||| ||||||||||| || || || || ||| | ||
--tgaggtcatttgggaaattgatggcattaatattctagtagcacccttactg---attatgtgaagacgtgatgccgttttgattcttttgattttgata--cagTGGTGAGAGTGGAGCAGGAAAAACAGAAACCGCAAAAATTGCTATGCAGTACCTGGCTTCCCTTGGAGGTGGAAGTGGCATTGAATACGAAATTCTTCAG
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 6
-----gacaagctctttcttggtgttccttaatcttgtgtgccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
||| | | || || | || | | | | | ||| |||||| || || || | || | || | | ||| |||||| |||||||||||||| ||||||||||||||||| ||||| ||||| ||||||||||| ||||| ||||||||||| || ||||||||||| |||||
agtgcgactatggaaaatagtggattggttgaaagaatgagttcttccactttgtgcat--cttgaagtgttttct-tatcacaagatttctttttcat--ccagTGGAGAGAGTGGAGCAGGAAAGACTGAGACAGCAAAGATAGCGATGCAATACTTGGCTGCTCTTGGAGGTGGAAGTGGGATCGAGTATGAGATACTAAAG
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 7
---------------------gacaagctctttcttggtgttccttaatcttgtg-tgccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
|||| | ||| | | ||| ||| ||| | ||||||||| ||| || ||| || | || | || | | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || ||||| || ||
gtaaagttgcattagttgtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtatt----ttgtggtgtatcct-tatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT-------------------
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 6
----gacaagctctttcttggtgttccttaatcttgtg-tgccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
|||| | ||| | | ||| ||| ||| | ||||||||| ||| || ||| || | || | || | | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || ||||| || || || |||||||| | |||
gtgagacactgagactagtggatctgttgaataaagtggtgcttccagtttgtgtatt----ttgtggtgtatcct-tatcacaagattctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 5
gacaagctctttcttggtgttccttaatcttgtgtgccccttaattgt--gtattgtgcttgaattgggacctataataat---agtta--tcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
|| | || ||| | | ||| | ||| | | || ||| ||| |||| ||| | ||| | | | || | | | |||||| || |||||||||||||| |||||||| ||||| ||||||||||| || |||||||||||||| || || || |||||||| |||||||| || ||
------cttaaaatcgg-gttatatcaagttgagaaccctgaattggttagtaaaactattgtattgaatccttgataaatctaaatcaattcttttgttcttccagTGGTGAAAGTGGAGCAGGGAAAACTGAGACGGCAAAGATAGCAATGCAATATTTGGCTGCCCTTGGTGGCGGTAGCGGAATAGAATATGAGATATTGAAA
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------gacaagc-tctttcttggtgttccttaatcttgtgtgccccttaattgtgta--ttgtgcttgaattgggacctataata-----atagttatcatgta--catgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
|| || |||| || || ||| | | | | | || | || ||| | | | ||||| | | ||| |||| | ||| |||||| |||||||| ||||| ||||| || || ||||| || || |||||||| |||||||| || || || || ||||||||||| |||| |||||| |
gtagtttatgtcccttgattcggtgctatattaattttcaaactacgagtatcttcttttgttttcaatcagcgaccacgttgtgcatttatttagacagtgtcctcttcgatagctatatgatgtacacggttttcatattactgtgtacagTGGTGAGAGTGGCGCAGGTAAGACAGAAACGGCAAAGATTGCTATGCAGTATTTGGCTGCTCTAGGAGGAGGTAGTGGAATAGAAGATGAAATTTTACAA
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ05534 (Selaginella moellendorffii), 3'ss of exon 4
gacaagctctttcttggtgttccttaatcttgtgtgccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
| | ||| || ||||| | | || || | |||||||| |||||||| || || ||||| || |||||||||||||| ||||||||| | ||| | |||| || ||| |||| ||||| |||| || | |
-------------------------------------------gtgaggagttgc-ctggaatttatgtgatgcactgtttcaatgctgatacttttcagTGGCGAGAGTGGTGCTGGAAAGACGGAAACAGCAAAAATAGCTATGCAGTACATCGCTACATTTGGTGGAGGACGTGGCGTAGAGGATGAAATCCTTGAA
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ25955 (Selaginella moellendorffii), 3'ss of exon 4
gacaagctctttcttggtgttccttaatcttgtgtgccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
|| | ||| || ||||| || | || || | |||||||| |||||||| || || ||||| || |||||||||||||| ||||||||| | ||| | | || || ||| | || ||||| |||| || | |
--------------------------------------------gtgaggatttgcctggaatttatgtgatgcattgtttcaatgctgatacttttcagTGGCGAGAGTGGTGCTGGAAAGACGGAAACAGCAAAAATAGCTATGCAGTACATCGCTACATTCGGTGGAGGACGGGGCGTAGAGGATGAAATCCTTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
tataataatagttatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacaagctctttcttggtgttccttaatcttgtgtgccccttaattgtgtattgtgcttgaattgggacctataataatagttatcatgtacatgttcagTGGGGAGAGTGGAGCAGGGAAGACTGAGACAGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGCGGTGGAAGTGGAATAGAGTATGAGATTTTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - cttggtg
- - - - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - tgcccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttga