Sequence
atgc intronic sequence ATGC exonic sequencegtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
Basic information
species | Glycine max |
transcript | GLYMA09G37610.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
||| | | | ||| || | ||| | || | | || | ||| | | | | | | || | | | | || |||| || ||||||||||| | |||||| |||||||||||| | || || || || |||||||||||||| ||||| || |||||||||| |||
---------------------------------------------------tttggagagcttttgcatt---gagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggatttttt-cagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
| | ||| | | | | |||||| | | |||||| || || | | | ||| || || || | ||| | | | | | | |||| || || || || || |||||||| || ||||| ||||| || || ||||| ||||||||||| || ||||||||| | ||||||||||||
--------------------------------------------------gtcgtaaggctatctggaatagttttttttttctggattatgttttggttgaagcttggctttgac----gagtttttgactgacagtctaccctg-aaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
| || || ||| | || | | ||| || ||| | | | | | | ||| |||| || | | || | |||| | ||| |||||||| || |||||||| || |||||||| ||||| ||||| ||||| |||||||||||||| ||||| ||||| ||||||||||||
------------------------------------------atgctgcatggctttccacctgctgatgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactgacaatcttcctggta----aacaca--------gGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 8
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
||| | | | | | ||| |||| || || | |||| | ||||| || ||| | | |||| ||| | || || |||| | || ||||| ||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||| ||||| |||||||| | |||||||| |||
-------------------------atgtaatgcctatggtagtcttttgccttttccatcattttcatttttcacttttt------------atttttatcatcagttgatca------agcttcttgtcaattt-----------ataatagGTGTATACAGTTGGCCCTGAATATGCACATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGCGTTGTTATGAGAAACCCCGATGGGAAAGAA
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacat--ttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
| ||| | | ||| ||| || | | | || | | ||| || || || ||| || | || | | || || |||| |||||||| || || |||||||||||||| || || || ||||||||||| || |||||||| || ||||||| | ||||||| |||||
----------------------------------------------------acatctgttagctttggcaaggactttggtcgattcgcct--ttttcatgtgtgaattt-caagac-gagattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ19878 (Selaginella moellendorffii), 3'ss of exon 8
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacattt-caacatatga-ttgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
|| || | || || | | || | | | ||| || ||||||| || ||||| || ||||||||||||||||||||| | || || ||||| ||||| || ||||| |||||| | | ||||| || ||
----------------------------------------------------------------------------------------------------------gtagacaactcaacttcttgttcttagcagccgcctcttctgaactgcagGTATACACTGTTGGACCAGAATATGCTCATGCTGAGGCACGAAAATCACCTGTTGTTGACGGGGTTGTTTTGAGAAGTCCCGATGGAAAAGAG
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 8
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacattt-caacatatga-ttgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
|| || | || || | | || | | | | ||| || ||||||| || ||||| || ||||||||||||||||||||| | || || ||||| ||||| || ||||| |||||| | ||||||| || ||
----------------------------------------------------------------------------------------------------------gtagacaactcaacttcttgttcttagcagtcgcctcttctgaactgcagGTATACACTGTTGGACCAGAATATGCTCATGCTGAGGCACGAAAATCACCTGTTGTTGACGGGGTTGTTTTGAGAAGTCCTGATGGAAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
ttctaaa putative branch site (score: 2)
aaattattttcaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
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