Sequence
atgc intronic sequence ATGC exonic sequencegtaagccttttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
Basic information
species | Glycine max |
transcript | GLYMA04G37050.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 23
gtaagccttttgca--caaatgtttttaatttgtatc---aattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
||||| ||| | | | || | || | | | | || || | | ||| | || | |||||||||||||| |||||||||| ||| | ||||| ||||| || ||||| || ||||| || ||||||||||| || ||||||||||||||||| || | ||||
gtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtgttgtatagGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATGCGTAAAATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 23
gtaagccttttgcacaaatgtt--tttaatttgtatca---attcatctgct-gcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
||| || || ||| ||| ||| ||| || | ||| || || | | || | || |||| | | | | | | ||||||||| ||| | || ||||| || ||||| ||||||||||| || ||||| ||||||||||| ||||| |||||||| |||||||| |||||||| |
gtatgc-ttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatgatccatacaaaa----tgcaacatttggca--gGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAAAACGAATTTATGGTGAATTGGGATGGATTACGCACTA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
-----gtaagccttttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaa-------aacttgtatggcttc--ttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
| | ||||| | | || | | ||| | || | | | | ||| | | || ||| ||| || | ||||||||| ||||| |||| || ||||| || || ||||| ||||| || ||||| |||||||||||||| || ||||| || |||||||| | | ||||
tgtgaatcactcttttttatat-tgcctatgattca-gcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
------------gtaagccttttgcaca---aatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
| |||| || ||||| | || || | | || | | | | | | || | | | | ||||||||| |||||||||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || ||||||||||||||||| | | ||||
acttactccacctctgggactttgaacgtccaatgtggagagcctgg--cagccgaggaggtgggaggctttcctgctcatttatcc-tgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G370521_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gtaagccttttgcacaa----------atgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgta-tggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
|| || || || | || | | || ||||| | || | || ||| | | | || | || | | | | ||||||||| |||||||||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || ||||||||||||||||| | | ||||
gtacgtactggtctaattaaaggtgcatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatatgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G417650_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gtaagccttttgcacaa----------atgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgta-tggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
|| || || || | || | | || ||||| | || | || ||| | | | || | || | | | | ||||||||| |||||||||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || ||||||||||||||||| || | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagcattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G482077_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gtaagccttttgcacaa----------atgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgta-tggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
|| || || || | || | | || ||||| | || | || ||| | | | || | || | | | | ||||||||| |||||||||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || |||||||||||||||| | | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttattctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGATCTGAGAACAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
gtaagccttttgcacaaatgtttttaatt-tgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
|| || ||| | || || | || | | | || | | | || | | | | || | || | | | ||||||||| ||||| |||| || | || ||||| ||||| |||||||||||||| |||||||||||||| || ||||||||||||||||| | | ||||
gttagtgattttcttaacggtcactgatgatatgcctatg-acataataagttgtagcttactcattgatt-tgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
----------------------------------------------------------gtaagccttttgcacaaatgtttttaattt-gtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
| | | | | || | ||| |||| ||| ||| | | | | | | ||||| | || || | ||||||||| ||||| |||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || ||||||||||||||||| | | ||||
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgc-tcatttatcctgctcttgttt---ttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gtaagccttttgcacaa----------atgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgta-tggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
|| || || || | || | | || ||||| | || | | || ||| | | | || | || | | | | ||||||||| |||||||||| ||| |||| || || || || ||||| |||||||| |||||||||||||| || ||||||||||||||||| | | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
gtaagccttttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
||| || ||||| | |||| | || | | | | | || ||| | || | || | || ||| || | ||| ||||| ||| | || ||||| |||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| || |||||||| || ||||| |
gtatgcaa---gcacacaagttt---actttagtaaccactaccggcacagtatataccaactt---tttttttgactttctgca--gGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 3
gtaagccttttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
||| || ||||| | |||| | || | | | | | || ||| | || | || | || ||| || | ||| ||||| ||| | || ||||| |||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| || |||||||| || | ||| |
gtatgcaa---gcacacaagttt---actttagtaatcactaccggcacagtatataccaacttctttttttttgactttctgca--gGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCACACTA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 14
gtaagccttttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
| || | || ||| ||| || | || | || || | || | | | || ||| || | ||| ||||| ||| | || ||||| |||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| || |||||||| | ||||| |
-----gtatgcaagcagacaggttacattagta--aacactgttggtacagtgtacaccaactg-----tctttgactttctgca--gGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 2
gtaagccttttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
||| || ||||| | |||| | || | | | | | || ||| | || | || | || ||| || | ||| ||||| ||| | || ||||| |||||||| ||||||||||| || |||| |||||||| |||||||| ||||| || |||||||| || ||||| |
gtatgcaa---gcacacaagttt---actttagtaaccactaccggcacagtatataccaacttc--tttttttgactttctgga--gGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCACAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G438355_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------gtaagccttttgcacaa--atgtttttaatttgt-atcaattcatctgctgcaaaataaatcagttaaaacttgt-atggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
| || ||| | || ||| || ||||| ||||||| | || ||| | | | || | ||| | | | | ||||||||| ||||| |||| ||| ||| || ||| | || ||||| |||||||| |||||||||||||| | ||||||||||||||||| | | | ||
gtaagttatagtagtgttgtgattcatgtacattttctacttatttcaattgtactaggacaccaccatatttgtagtttgttgtcaattc-catattgatgcatactttcttgctcatttatcatgccctagtttttagGTTGATGGCATGCTGGGAAGGCAGGAGAACCCTAGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTCTATGGTGAACTGGGATGGTCTCAGAAGAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 23
gtaagccttttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagt-taaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
|| ||| || | || | ||||| ||| ||| | | |||| | | | || |||| ||| | ||||||||||||||| ||||| ||||||| ||||| ||||| |||||||||||||| ||||||||||| ||||| ||||| |||||||||||||| |||||||
gtgagc--ttcatataactctttttg-tttatata---ttgtttgcttcctctctgcttgctatattctttgtttggtct------tagGTTGATAGCATGCTGGGCCGGAGGGAGAATCCAGGGGAACATGAGGCCATGCGTAAGATGAAAAACGAATTTATGGTCAACTGGGATGGCTTGCGCACAAMapped 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|16283953|gb|BI945829.1|BI945829EST: TTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTT-ACGAA GTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGTGGAGCATGAGGCCATG
genomic: TTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAAgtaagccttt ... tcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG
EST:
gi|10845533|gb|BF071131.1|BF071131EST: TTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA GTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG
genomic: TTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAAgtaagccttt ... tcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
cttcttgt CT-rich tract
aaaataaatcagttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagccttttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG