Sequence
atgc intronic sequence ATGC exonic sequence...tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
Basic information
species | Glycine max |
transcript | GLYMA07G05390.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 3
--tattc-atgcaa-aactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
| ||| | || | | | | || | || || | || || ||| | || || | |||| | | | | | |||||||| |||||||| ||||||||||| || ||||| || |||||||| || |||||| | ||||||
attgttctgtttaacgattctagaagctttatctacagtcggttcctgacagtgcatgcaacctaca--tggttaatggcttccatttatatcaca--ccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 2
tattcatgcaaa-actgtcactccattcttgaccagaaat--ttcctactatgtatgttatttatgcttgttcaa---tgcttacttgctcagttgc-tatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
| || | || | ||| | ||| || ||| | | || || ||| |||| || ||| | | || ||| | |||||||||||||| | |||||||||||||| || ||||| || ||||| || || || || || | |
-------gtaagcgccctcgccacatgccacgccacaagggattcttcccttggat-ttacactcacttgactaacgatgcgtttcttcttggttttgcgtggatagGTTGTGGAGATCTCCAAGGGAAGCAAGGTGAAGTACGAGCTCGACAAGAAAACGGGGTTCATCATG
upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 3
-tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
| || | | |||| | || || | | | | || || ||| ||||| | | | | | | | |||||||| |||||||| ||||||||||| ||||||||||| |||||||| || |||||| | ||||||
ttgttgaggaaaaataagtgcatggtttttttttaattacgatatttaacaaat-ctagttagctccaaacaatgaccgcgttatataattttttattcagGTTGTTGAGATCACAAAGGGAAGCAAAGTCAAATACGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 3
-tattcatgcaaaactgtcac-tccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
| | | || | | | | |||| || | || || || || | | | || || | | || || | | | | || | |||||||||| |||||||| ||||||||||| || ||||| || |||||||| || |||||| | ||||||
atttgcttgtcgagcaaaaaagtgcattttttatcataatgtt--taacaaatctactagttcgcttcatacagtgactgcattatttacatctttatgcagGTTGTTGAGATCACAAAGGGAAGCAAAGTTAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G026470_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------tattcatgcaaaactgt---cactc--cattcttgaccagaaa---tttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG----------------------------------
| || |||| ||| | || ||| ||| | | | || || || | | | || | |||| | | || | | |||||| ||||||||||| ||||| |||||||| || ||||| || ||||| ||||| || | || |||
gtaagtatctgacgaatcccattccccagacccctcaccccagcaagcaagcaagcaagcagccaaagttgttctcgatcgacatgtgtgaatatggagcgtgtctgacgatccttccggtgcgcgtccgtccgtccgttacgtacgtggtgccgacgagcagGTCGTGGAGATCACCAAGGGGAGCAAGGTGAAGTACGAGCTGGACAAGAAGACGGGGCTCATCAAGGTGGACCGGATCCTCTACTCGTCCGTCGTCTACC
upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
|| | | | | |||| ||| | | ||||| ||||||| | || | ||| || | | | || ||| ||||||| ||||||||||| |||||||||||||||||||| |||||||||||||| ||| | || |||
---------gtaagttttttcctactctttgttctaaa---cagagtatgt-tgttatta--gattctctaatcattttatctttggatg--attattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
upper sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatg-tatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
| |||| || | | | ||| | ||| || | | | | | |||| || || | || | || || | ||||| || |||||||| ||||||||||| || ||||| ||||| ||||||||||| || | || |||
----------gtattgtctcttaacttataacccaagtaagccttctttaatctctctctctctcttggtc--tgttaacgagag-agcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAGMapped 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|17400209|gb|BM176991.1|BM176991EST: GACCTGGAGCGCCTATGATTTTCAATTGT GTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
genomic: GACCTGGAGCGCCTATGATTTTCAATTGTgtaagttctg ... ctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
EST:
gi|48574801|gb|CO036084.1|CO036084EST: GACCTGGAGCGCCTATGATTTTCAATTGT GTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
genomic: GACCTGGAGCGCCTATGATTTTCAATTGTgtaagttctg ... ctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
tgcttac putative branch site (score: 2)
tatgttatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- -tcatgca
- - - - - - - - -cactcca
- - - - - - - - - - - - - cttgacc
- - - - - - - - - - - - - - - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacttgc