Sequence
atgc intronic sequence ATGC exonic sequence...gaatattcaaatattgcatcatgggtcatgcatgacatgaatcacggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
Basic information
species | Glycine max |
transcript | GLYMA16G02200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g02300.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------gaatattcaaatattgcatcatgggtcatgcatga---catgaatca-cggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
||| |||| | | | || ||| || ||||| | |||| | | | | || | | | | | | | ||||||||| || || || || | |||||||| || |||||||||||||||||||| |||||||||||||| || || ||| | || || | || || ||
gtagctaagctagtattcctcatcatataacctttctcctctccaattctcaatttctagctaccaaatcgatgatggatttatcaatcaatcgagctaagctagctaagtaatggtgtgtgtgcaaaatatatattgtggttgcagAGAGGTGTAAGATTGGGTCAGGGCCGCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGGC
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g04090.1 (Oryza sativa), 3'ss of exon 1
--gaatattcaaatattgcatcatgggtcatgcatgacatgaatcacggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
|| | || | ||| | ||| || || | | || | | || | || || | | | | | | | |||||||| |||| || || | ||||| || || |||||||||||||||||||| |||||||||||||| || || ||| | || || || ||||| ||
gtacgtaattaagcacacacacatcgatca-attcgat-cgatttttgacatgttttgatcaatgtggcatgtgtgtatcatacatacata------tgcagAGAGGTGCAGGATTGGGTCAGGGCCGCAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCAACGGC
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G069047_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------gaatattcaaatattgcatcatg-ggtcatg--catgacatga--atcacggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
| | | | ||| | |||| | ||| ||| ||| | | || | | |||||| || | || | | | ||||||| |||||| || || | ||| ||||| || |||||||||||||||||||| |||||||||||||| || || ||||||||||| ||||| || ||
gtacggtatacttaccaccatataccttccatctccgaggtccgagcaaagcatcagctcgtgatcataggatcggatcggagctggtgacctgatggtcatgtcacacgagcatgaacgtgagctgatcatcgtacgtccatggcgctgatcatcggggttagttatcgattctgcgtgcat---gcagAGAGATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCTACGGC
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G171395_T01 (Zea mays), 3'ss of exon 1
---------------------------------------gaatattcaaatattgcatcatgggt-catgcat--gacatgaatcacggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
| ||| ||| |||| | ||||| | | | | || | | | | || | | | || | | ||||||||| ||| || || | || ||||| || |||||||||||||||||||| |||||||||||||| || || ||||||||||| ||||| || ||
gtagtactacgctgttacgcacgcacgcgcttgcttgctgcatacatgtctatgcggccatgcatacatgcctctgccgtccgtctgccctccccgatgcatatatggccgatcctgatcgtcgagccggtgaccgatgcagAGAAGTGCCGCATCGGTTCGGGCCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACCGC
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
gaatattcaaatattgcatcatgggtcatgca-tgac--atgaatcacggc-actaatgc-accattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
||||| || || || | || || | || | ||| | | || | | | | || | || |||||||||||||| || || | ||| ||||| || |||||||||||||||||||| |||||||||||||| || || ||||||||||| ||||| || ||
-----atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
------------gaatattcaaatat-tgcat-catgggtcatgcatga----catgaatcacggcactaatgcac-cattttgaggggtttcttttttcttttctttatt---ttttgcagAGAAATGCAAAATAGGAACCAC------TCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
| |||| | || || | | | ||||||||| | | ||| | || ||| || | | || | | | | |||||| || ||| | || | | || ||||| || |||||||||||||||||||| |||| ||||||||| || || ||||||||||| |||||
gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0048g02660.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------gaatattcaaatattgcatcatgggtcatgcatgacatgaatcacggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
| | ||| ||||| || || ||| || | || || || |||| | ||| | | || | ||||||||||||| || | ||||||| |||| || || || ||||||||||||||||||||||| |||||||| || || || ||||| | || |||||||| |||||
gttgtgcttcatatttagttcatcgcctctcattcttttctcttaattttgcaattcttgttgaatattccatcaag-atagcgtgtatcttcccctttgtgatgttcatatcggct-----tgggtttttgcagAGAAGTGTAGAATAGGATCCACCCCTCAAAACGATTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCAACGGGAACCAGGACTAATCGCGCCACTGC
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------------------gaatattcaaatattgca-tcatgggtcatgcatgacatgaatcacggcactaatgcaccattttgaggggtttcttttt----tcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGC---------AGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
| | | || |||| | |||||| | | | | || | ||| | | |||| | | | | | | | | | |||| |||| || || | || | | || || |||||||||||||||||||||||||| ||||||||| | || | || | || ||
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctggg--attgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------gaatattcaaa----tattgcatcatgggtcatgcatgacatgaatc--acggcactaatgcaccattt----------tgaggggtttcttttttctt--------ttctttattttttgcagAGAAATGCAAAAT-AGGAACCACTCCGCAGAA--------TGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
|| ||| ||| || | || | || |||| | | ||| | ||| | ||| | | | | || | || |||| |||| || || || || | |||| ||| |||||||||||||||||||| || |||||||| |||||||||| || |||| ||
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
---------gaatattcaaatattgcatcatgggtcatgcatgacatgaatcacggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAAT----AGGAACCACTCCG-----CAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
| | |||| | | | |||||| | || | || | | | ||| || || || | | | ||| |||||| |||||| || | |||| |||| ||||| | ||||||||||| ||||| || ||||||||||||||||| || | ||| |||| ||
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatg---tacattgtaat-ccaaggaagagtattg-ggcattgctaactgatagcgtccatt----gcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
-----------------gaatattcaaatattgcatcatgggtcatgcatgacatgaatcacggcact---aatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
|| ||| || | | | | | | || || | |||| | | | | | || ||| |||| ||| ||| || || | |||| | || ||||||||||||||||||||||||||||| ||||| || || ||| | ||||| | || || |
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
gaatattcaaatattgcatcatgggtcatgca-tgacatgaatcacggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
|| | | | | | || || | | ||||| ||| ||| | ||||| |||| |||||||| || || || ||| | || || | || |||||||| ||||| ||||| ||||||||||| ||||| ||||| |||||||| | || || ||
------------------------gtagtctagtctcctccatttcgatatgattgcacaccactgaca---cctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
----------gaatattcaaatattgcatcatgggtcatgcatgac--------atgaatcacggcact---aatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
| |||| | ||| ||| | | || | || || | |||| | | | | | || ||| |||| ||| ||| || || | |||| | || ||||||||||||||||||||||||||||| ||||| || || ||| | ||||| | || || |
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
gaatattcaaatattgcatcatgggtcatgca-tgacatgaatcacggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
|| | | | | | || || || | | ||| ||| ||| | ||||| |||| |||||||| || || || ||| | || || | || |||||||| ||||| ||||| ||||||||||| ||||| ||||| |||||||| | || || ||
------------------------gtagtctagtctcctccatttcgacatgattacacaccactgaca---cctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGCMapped 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|22930838|gb|BU547985.1|BU547985EST: CGAGCCATGGGACATACAAG AGAAATGCAAAATAGGAACCACTCCGCAGAATGATTNNNACTTCTTCAGCC
genomic: CGAGCCATGGGACATACAAGgtgtgataga ... ttttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
cactaat putative branch site (score: 2)
tttcttttttcttttc putative PPT
tttcttttttcttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatattcaaatattgcatcatgggtcatgcatgacatgaatcacggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - -tattgca
- - - - - - - - - tcatggg
- - - - - - - - - - - - - - -gcatgac
- - - - - - - - - - - - - - - - - - - - - cacggca
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagggg