Sequence
atgc intronic sequence ATGC exonic sequence...accttcctacctttaaaaatatagaggaaaaacttttgacaataaactttatcttgtgtttccccatgcttgctccttcatgcaatttacatttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC
Basic information
species | Glycine max |
transcript | GLYMA02G43910.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 4
----accttcctacctttaaaaa-tatagaggaaaaacttttgacaataaactttatcttgtgtttccccatgcttgctccttcatgcaatttacatttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC
| ||| | | ||| | | | | | || ||| || | | | || | || | || || | |||| | |||| | |||| ||||| | ||| |||| ||||||||||||||||| | ||||||| |||||||||||||| | || || ||||| || || ||||| || || |
actcatctttaaaattggaaagcctctggtgaaggaagattttgtaactgattatgactgaagagcaatgata--tactaattgac-caatgttgattttt--agGTCCTTGTGCGGAATATACCGCCTGATCCTGATGAATCAATTGGTGAGCTTGTGGAACATTTCTTCCTTGTAAACCATCCTGACCATTATCTTACGCACC
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G456000_T01 (Zea mays), 3'ss of exon 4
---accttcctacctttaaaaatatagaggaaaaacttttgacaataaactttatcttgtgtttccccatgcttgctccttcatgcaatttacatttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC
| |||| || | | || | | | ||| || | | ||| ||| | || || | | || | | | | |||| ||||| | ||| ||||||| |||||||||||||| |||||||||| |||||||||||||| | ||||||||||| ||||| ||||| || |
aatatcttcatatcaggactaactttacatagctg-tcatgataagttgatgcacctttagttcgcaaattctaagttactaatttg-ccaatgtgttt-tagGTCCTTGTGCGGAATATACCACCAGATCCTGATGAATCAATCAGTGAGCTTGTGGAACATTTCTTCCTTGTCAATCATCCTGATCATTATCTACAACACC
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G163334_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------acc-ttcctacctttaa---aaatatagaggaaaaa--------cttttgacaataaactttatcttgtg--tttccccatg-------cttgct-ccttcatgcaatttacatttgtg---cagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC
|| || || | ||| | | || | |||| | | ||||| | || | ||| ||| ||| ||| |||| | | | | | | || | |||| ||||| | ||| |||| |||||||| |||||||| | |||||||| ||||||||||||||| | || |||||||| | ||||||||| || || |
gtatgactaacctatgattgagttatgccttgaacacatagtgctatccagacacttaaagttgaaatttgtactgttactgcatttcacatagattttgaggcgagaacacgtttcttttttcccctaaactgatcaagtggattttgttatgggtatgacttgttgtatgcgcttactcaatgattatattttagGTCCTTGTGCGGAATATACCGCCTGATCCAGATGAATCAATTAGTGAGCTTGTGGAACATTTCTTTCTTGTGAATCATCCTGGTCACTATCTGACACATC
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------acc-ttcctacctttaa---aaatatagaggaaaaa--------cttttgacaataaactttatcttgtg--tttccccatgcttgctccttcatgcaatttacatttgtgca--------------gGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC
|| || || | ||| | | || | |||| | | ||||| | || | ||| ||| ||| | | | | | ||| | | | || || ||| ||||| | ||| |||| |||||||| |||||||| | |||||||| ||||||||||||||| | || |||||||| | ||||||||| || || |
gtatgactaacctatgattgagttatgccttgaacacatagtgctatccagatacttaaagttgaaatttgtactgttactgcatttcacatagattttgaggcgagaacacgtttcttttttcccctaaactgatcaagtggattttgttgttatgggtatgacttgctgtatgcgcttactcaatgattatattttagGTCCTTGTGCGGAATATACCGCCTGATCCAGATGAATCAATTAGTGAGCTTGTGGAACATTTCTTTCTTGTGAATCATCCTGGTCACTATCTGACACATC
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G15430.1 (Arabidopsis thaliana), 3'ss of exon 4
accttcctacctttaaaaatatagaggaaaaacttttgacaataaactttatcttgtgtttccccatgcttgctccttcatgcaatttacatttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC
| || || | | | || | |||| || || | | ||||||||| || ||| || || | | | ||||||| || ||||| | || | |||||| ||||||| | |||| || || ||||||||||| ||||||||||||||||||||||||||| |
gtaatgaaactttgctacctgttgatg-----ttttttactctatgacaaaac---catttccccatagctgaaacttgttg-aactgtcttcatcttagGTACTGGTAAGAAACATTCCTGCAGATCCTCATGAATCAATATGTGAACTTGTTGAACATTTCTTCAAAGTCAATCATCCAGATCACTATCTCACTTTCC
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G21620.1 (Arabidopsis thaliana), 3'ss of exon 4
accttcctacctttaaaaatatagaggaaaaacttttgacaataaactttatcttgtgtttccccatg------cttgctccttcatgcaatttac--atttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC
|| | | | ||| || | | | ||||| ||| |||| | | | || | | || | |||| || || |||| ||||| || || | || || |||||||||||||| || |||||||| || || ||||||||| |||||| |||||||| |||| |||||| | |
------------gtatgcagacattttaaatctcttggtccacttacttt---ttgagttttctgaagaggaaatgtggtatgtgattctattttttgatgaatgtagGTTCTTGTAAGGAACATTCCTCCAGATCCTGATGAATCAGTAAGTGAGCTCGTTGAGCATTTCTTTAAGGTCAACCATCCAGACTACTACCTCACTTACC
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0059g01090.t01 (Vitis vinifera), 3'ss of exon 3
--accttcctacctttaaaaatatagaggaaaaacttttgacaataaactttatcttgtgtttccccatgcttgctccttcatgcaatttacatttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC
| || | |||| | || | | | | | || | ||| ||| | | | |||| | ||||| ||||| |||| |||||||| ||| |||| ||||| ||||| || |||||| ||||||||||| || |||||||| ||||| |||||| | | | |
atgtatagttagtcacacaaatttgagtagtaatgctcctgtattgttgtctttccaattactcctttaacttcatgcattgcaaaatt--cttttgtacagGTGATTGTGAGAAATGTGCCATCTGACCCTGACGAATCAGTTCTTGAGCTTGTGGAACATTTTTTCTTGGTCAACCATCCCAATCACTTTTTGGGTTTTCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|209701364|gb|BW655960.1|BW655960EST: TGAGATTGCATTTTCTTGCATCAGAACGACGCCGTCCTGACCAATTTACA GTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTA
genomic: TGAGATTGCATTTTCTTGCATCAGAACGACGCCGTCCTGACCAATTTACAgtaagatcaa ... atttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttatcttgtgtttccccatgcttgctccttcatgcaatttacatttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC
aatttacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accttcctacctttaaaaatatagaggaaaaacttttgacaataaactttatcttgtgtttccccatgcttgctccttcatgcaatttacatttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA