Sequence
atgc intronic sequence ATGC exonic sequence...cctacctgctttagaagaaaaaaatgttactctggaatccatatttgcttttccatggatttttccgtaagtaatgtcaaaatgggttcaaaatggctagGTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGTTTTTGGATGAATTTTCCTAAAGAAGGT
Basic information
species | Glycine max |
transcript | GLYMA13G20980.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 2
cctacctgctttagaagaaaaaaatgttactctggaatcca-tatt-tgcttttccatggatttttccgtaagtaatgtcaaaatgggt---tcaaaatggctagGTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGTTTTTGGATGAATTTTCCTAAAGAAGGT
|| | | || | | || | | | || ||| || | | ||| | | || | | | | || | | | || |||||| || || ||||||||||| || || |||| ||| ||||| || || |||||||||||||| |||||||||| ||||||| || || ||||||||
----ttaagttaaaatgagagttttcctagttagtaggacaatatgatggtgatacatcagtaataat-tatatcctataatgatcaatgcattattgtgtttagGTACACGGTAGGAAAGATTACGCCCATTCAGAAACGTGAAGTCCGTGCTTCAGATTTTGGTCCACGAGCAAGTTTCTGGATGACCTTCCCCAAAGAAGGA
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G076392_T02 (Zea mays), 3'ss of exon 1
cctacctgctttagaagaaaaaaatgttactctggaatccatatttgct-tttccatggatttttccgtaagtaatgtcaaaatgggt--tcaaa-----atggctagGTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGTTTTTGGATGAATTTTCCTAAAGAAGGT
|| | ||||| || | | | | | |||| | || | || || || || | ||| || || || | | | | || |||||||| || |||||||||||||| || |||||||| ||||| ||||| || |||| |||| | ||||||||||| |||||||| || || ||| | |||
------tggtatagaaaaatgtaccagaatgttctagt--atatctactatcaacagggcattgtcttattgaaatatccaactgaatgattatacatttatactcagGTATACAGTTGGAAAGATTACACCTATTCAGAGACGTGAAGTGCGAGCTTCTGATTATGGTTCCAGAGCAAGTTTCTGGATGAACTTCCCCAAAAATGGT
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 2
cctacctgctttagaagaaaaaaatgttactc--tggaatccatatttgctttt-ccatggatttttccgtaagta-atgtcaaaatggg-----ttcaaaatggctagGTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGTTTTTGGATGAATTTTCCTAAAGAAGGT
| | | | | | | ||| | | ||||| | || | | |||| || |||||| || ||||| || || | |||||| || || |||||||| |||||||| || | ||| |||||||| || ||||||||||| || ||||||||||| |||||||| || || ||||||||
-------gatcctgcaacgtacatttttatttaattaaatccgaagttatgatggttacagattgttt--taagtatatttcaaaccggcaatgttttgttgtacttagGTACACAGTTGGAAAGATCACACCAATTCAAAAACGTGAAGTTCGTGCTTCAGATTTTGGACCAAGAGCAAGTTTCTGGATGAACTTCCCAAAAGAAGGA
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------------------cctacctgctttagaagaaaaaaatgttactc-tggaatccatatttgcttttccatggatttttcc----gtaagtaatgtcaaaatgggttcaaaatggctagGTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGTTTTTGGATGAATTTTCCTAAAGAAGGT
|| | |||| | | | | | | | | |||||| | | | | |||| || || | | || | |||| | |||||| || || || |||||||||||||| || | ||| ||||||| || ||||||||||| || | ||||||||| ||||||||||| | ||||||||
gtatgaactaatgcagtagtggttagttggttactgcattagtttcttactggctccaagcttgcaacctgcacttttcgtgttaggaactgctagcttctgcaacgtacattttctttaattaaatccagggtatgatgtttacagattgttttaggtatatttgaaatcggcaatggttttttgtacttagGTACACAGTTGGGAAGATTACACCAATTCAAAAACGTGAAGTTCATGCTTCAGATTTTGGACCAACAGCAAGTTTCTGGATGAATTTCTCAAAAGAAGGA
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 1
cctacctgctttagaagaaaaaaatgttactctggaatccatatttgcttttccatggatttttccgtaa-gtaatgtcaaaatgggttcaaaatggctagGTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGTTTTTGGATGAATTTTCCTAAAGAAGGT
||||| ||| | | ||| | | | ||| | | || || || || | | || ||||||| | ||| || || ||||| || ||||| |||||||| |||||| ||||||| || |||| ||||| ||| | || ||||||||||||| ||||||| || ||
---gtatgcttgctccttctaaacctgtgccctgtgagc-gtgtttagctctaaattcatcaccgaatattgttgttactgaactagttcaaac--gttagATACACAGTGGGGAAAATTACGCCAATACAAAGACGACAAGTTCGGACAGCAGACTTTGGACCTCGGGCTAGTTTTTGGATGACTTTTCCTCGAGCTGGC
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 1
---cctacctgctttag-aagaaaaaaatgttactctggaatccatatttgcttttccatggatttttccgtaagtaatgtcaaaatgggttcaaa-atggctagGTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGTTTTTGGATGAATTTTCCTAAAGAAGGT
|| || || || ||| | || || ||| | || | || || || ||| | | | | || | ||| | || || || ||||||||||| || ||||||||||||||||| ||||| ||||| ||||||||||||||||| ||||| ||||||||||||| ||||| ||||||||
aggcccacttgtcatatcaaggatgtaaatatatgctgatctttatgtctgtcattatat---tttactcatgattgctg--agtatgaaattgaatgtgatcagATATACTGTGGGGAAAATTACACCAATACAGAGGCGAGAGGTTCGTGCATCAGATTTTGGTCCCAGAGCCAGTTTTTGGATGAGCTTTCCAAAAGAAGGAMapped 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|208106375|gb|GD906444.1|GD906444EST: AGTTTACAGCTTGGAATAAG GTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATC
genomic: AGTTTACAGCTTGGAATAAGgtaaaagaca ... aaatggctagGTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttttccatggatttttccgtaagtaatgtcaaaatgggttcaaaatggctagGTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGTTTTTGGATGAATTTTCCTAAAGAAGGT
taagtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctacctgctttagaagaaaaaaatgttactctggaatccatatttgcttttccatggatttttccgtaagtaatgtcaaaatgggttcaaaatggctagGTATACTGTGGGAAAGATTACACCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGTTTTTGGATGAATTTTCCTAAAGAAGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
cctacct
- - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - -ctctgga