Sequence
atgc intronic sequence ATGC exonic sequencegtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
Basic information
species | Glycine max |
transcript | GLYMA19G02260.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
||| ||||| || | || | |||| | | | | | ||| | | | | | || | | || || | | |||| || ||||| || || | |||||| |||||||||||| | || || || ||||||||||||||||||||||| || ||| ||||||| |||
-----------------tttggagagcttttg-----cattgagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
|| | || | || | | | || |||| ||| | | | ||| | || || |||| | || | | || || | | |||| |||| || || || ||||| |||||||| || ||||| ||||| || || ||||||||||||||||| || ||||||||||| |||||||||||
--------gtcgtaaggct-atctggaata--gttttttttttctggattatgttttggttgaagcttgg----ctttgacgagtt---tttgactgacagtctaccctgaaata----cagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgta-tttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
||| ||| | |||| | ||||| || | || | || | | | | || | || || | | | | | |||| |||||||| ||||||||||| || |||||||| ||||| ||||| |||||||||||||||||||||||||| ||| | |||||||||||
--------------------atgctgcatggctttccacctgct---gatgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactgacaatcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 8
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
| | | |||| | | | | | ||||||| | | | |||| | ||| | | | || || | || || | || |||| |||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||||| |||
---------atgtaatgcctatggtagtcttt-tgccttttccatcattttcatttttcactttttatttttatcatcagttgatcaag-----cttcttgtcaatttataa-------tagGTGTATACAGTTGGCCCTGAATATGCACATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGCGTTGTTATGAGAAACCCCGATGGGAAAGAA
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
| | || || ||| | ||| | | || | | || | | ||| || | | | | | | || || ||||||||||||| || || |||||||| ||||| || || || |||||||||||||| |||||||| || ||||||| | || |||| |||||
--------------------acatctgttagctttggcaaggactttggtcgattcgcctttttcatgtgtgaatttcaagacg--agattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ19878 (Selaginella moellendorffii), 3'ss of exon 8
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
| | | | | | || | | | || |||| |||| || || || || || |||||||| |||||||||||| | || || ||||||||||| || |||||| |||||| ||| |||| || ||
-------------------------------------------------------------------gtagacaactcaacttcttgttcttagcagccgcctcttctg-----aactgcagGTATACACTGTTGGACCAGAATATGCTCATGCTGAGGCACGAAAATCACCTGTTGTTGACGGGGTTGTTTTGAGAAGTCCCGATGGAAAAGAG
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 8
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
| | ||| | || | | | |||| | ||| ||| | | || ||| |||| || || || || || |||||||| |||||||||||| | || || ||||||||||| || |||||| |||||| |||| |||| || ||
---------------------------------------------------------gtagacaactcaacttcttgt----tcttagca--gtcgcct------cttctgaa---ctgcagGTATACACTGTTGGACCAGAATATGCTCATGCTGAGGCACGAAAATCACCTGTTGTTGACGGGGTTGTTTTGAGAAGTCCTGATGGAAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
tagaattttcataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA