Sequence
atgc intronic sequence ATGC exonic sequencegtatgttcccaaccatttcctgcgttctgttctgctctgttcggttatgatagatccgttagtgttttctcttccgttttgcttttcttatgaatgaatgaatgcatgcttatattttgagtgaatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
Basic information
species | Glycine max |
transcript | GLYMA12G36940.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 1
-----------------------------gtatgttcccaaccatttcctgcgtt----ctgttctgctctgtt--cggttatg----atagatccgttagtgttttctcttccgt-tttgcttttcttatgaatgaatgaatgcatgcttatattttgagtgaatttgacagTTGAATTTGGAA----AACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
| | | | || | ||| || | | ||| ||| | | | | ||| | || | ||| ||||||||| | || || ||| | | | || | | |||| || | | ||| || |||||||| ||| | ||||||||||||||||| ||||| ||||| ||||| ||||| |||||||| | || || || |||
gtaaccatctcatccttcgcctcccctcgattcgctgctcgcctgcggcggcggcgcggctaggccatttcgttgccggcgtcggcctgcgggttcaccggtgggtgctttgccgcgtttgcttttgtcgtggatc--tgatggagtttgcgttttctcgcgggattttgtagGTAAGGGAGGAGGAGTAAGAAGATGTCGCACAGGAAGTTCGAGCACCCGAGGCACGGATCCCTCGGCTTCCTCCCGAGGAAGCGCTCCTCCCGCCACCGC----
upper sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g07010.1 (Oryza sativa), 3'ss of exon 1
gtatgttcccaaccatttcctgcgttctgttctgctctgttcggttatgatagatccgttagtgttttctcttccgttttgcttttcttatgaatgaatgaatgcatgcttatattttgagtgaatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA---
| | | | | | | || || | || | || | || ||| ||| | | |||| || || | || | | || || | ||| | || ||| | | | | |||||||| ||| | ||||||||||||||||| || || ||||| ||||| ||||| |||||||| | || || || ||||| |
---------------tcgctggtgctgtagtttgatcgctgtggct-tg------cgattggtgattttacgggcatttt--cttggttgcggatc--tcatggcttgtgtgggtttcg-------tttgcagGTAAG---GAGGAGGAAGATGTCGCACAGGAAGTTCGAGCACCCGAGGCATGGATCCCTCGGCTTCCTCCCGAGGAAGCGCTCCTCCCGCCACCGCGGCAAGG
upper sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G324314_T03 (Zea mays), 3'ss of exon 1
---gtatgttcccaaccatttcctgcgttctgttctgctctgttcggttatgatagatc-cgttagtgttttctcttccgttttgcttttc-----ttatgaatgaatgaatgcatgcttatattttgagtgaatttg-acagTTGA--ATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
| | | || | | | | | | | || | | || | |||||| ||| || || | ||| | || | || |||| | ||| | | | ||| || |||||| ||||| ||||||||||||||||| ||||| ||||| ||||| || || |||||||| | || ||||| |||||
gtaacgaatccgccgccggcgtcatctcctcctcccacctcgactcgccttgctcgccggcggcggccttttcttcgccgcgcggcgagtcgcccatgttgagctcgcggctgatctgatgggcttgttgtgatctcctgcagGTAAGGAAGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCGCGG--
upper sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G801409_T03 (Zea mays), 3'ss of exon 1
--gtatgttcccaa-ccatttcctgcgt--tctgttctgctctgttcggttatgatagatc-----cgttagtgttttctcttccg-------------ttttgcttttcttatgaatgaatgaatg--catgcttatattttgagtgaatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
| |||| | || || | |||| ||| ||| | | ||| | | | || || | |||||| ||| || | || || ||| ||| | || | || | | || | || || ||| || |||||| ||||| ||||||||||||||||| ||||| ||||| ||||| || || |||||||| | || ||||| ||
gtgaatgtaacgaatccgccgcgggcgtcatctcctcttcccacctcgactcgccttgctcgccggcggcggccttttcttcgccgagcggcgagccgcccatgttgagctcgtggctgatctgatgggcttgttgtgatctcctgcagATAAGGAAGAGGA----GGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCG-----
upper sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G132968_T01 (Zea mays), 3'ss of exon 1
------------------------gtatgttcccaaccatttcctgcgttctgttctgctctgttcggttatgatagatccgttagtgttttctcttccgttt-tgcttttcttatgaatgaatgaatg--catgcttatattttgagtgaatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
| | || | || | || | ||||| || | | ||| | ||| || | || | || ||| | || | || | | | | || || ||| || |||||| ||||| ||||||||||||||||| ||||| ||||| ||||| || || |||||||| | || || || ||
gtgaatataaggaatccgccgccggcgtcatctcctcctcccacctcgactcgccttgctcg--ccgtcggcggccatttcgtcgccgcgcggcgagccgcccatgttgagctcgcgtcggatctgatgggcttgttgtgatctcctgcagGTAAGGAAGAGGA----GGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGCCACCG-----
upper sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G324314_T04 (Zea mays), 3'ss of exon 1
--gtatgttcccaa-ccatttcctgcgt--tctgttctgctctgttcggttatgatagatc-----cgttagtgttttctcttccgttttgcttttc-----ttatgaatgaatgaatgcatgcttatattttgagtgaatttg-acagTTGA--ATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
| |||| | || || || |||| ||| || | | ||| | | | || || | |||||| ||| || || | ||| | || | || |||| | ||| | | | ||| || |||||| ||||| ||||||||||||||||| ||||| ||||| ||||| || || |||||||| | || ||||| |||||
gtggatgtaacgaatccgccgccggcgtcatctcctcctcccacctcgactcgccttgctcgccggcggcggccttttcttcgccgcgcggcgagtcgcccatgttgagctcgcggctgatctgatgggcttgttgtgatctcctgcagGTAAGGAAGAGGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCGCGG--
upper sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 3
------------------------gtatgttcccaaccatttcctgcgttctgttctgctctgttcggttatgatagatccgttagtgttttctcttccgttt-tgcttttcttatgaatgaatgaatg--catgcttatattttgagtgaatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
| | || | || | || | ||||| || | | ||| | ||| || | || | || ||| | || | || | | | | || || ||| || |||||| ||||| ||||||||||||||||| ||||| ||||| ||||| || || |||||||| | || ||||| ||
gtgaatataacgaatccgccgccggcgtcatctcctcctcccacctcgactcgccttgctcg--ccgtcggcggccatttcgtcgccgcgcggcgagccgcccatgttgagctcgcggcggatctgatgggcttgttgtgatctcctgcagGTAAGGAAGAGGA----GGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGTCACCG-----
upper sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G135727_T04 (Zea mays), 3'ss of exon 1
-----------------gtatgttcccaac--catttcctgcgttctgttctgctctgttcggttatgataga-------tccgttagtgttttctcttccgttt-tgcttttcttatgaatgaatgaatg--catgcttatattttgagtgaatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
| | || | ||| |||| | | || ||| | ||| | | | ||| | ||| || | || | || ||| | || | || | | | | || || ||| || |||||| ||||| ||||||||||||||||| ||||| ||||| ||||| || || |||||||| | || || || ||||| |
gtgaatgaatataacgaatccgccgccggcgtcatctcctcctcccacctcgactcgccttggtcgccgtcggcggccatttcgtcgccgcgcggcgagccgcccatgttgagctcgcggcggatctgatgggcttgttgtgatctcctgcaggtaagGAAGAGGA----GGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGCCACCGCGGCA
upper sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G135727_T01 (Zea mays), 3'ss of exon 1
-----------------gtatgttcccaac--catttcctgcgttctgttctgctctgttcggttatgataga-------tccgttagtgttttctcttccgttt-tgcttttcttatgaatgaatgaatg--catgcttatattttgagtgaatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
| | || | ||| |||| | | || ||| | ||| | | | ||| | ||| || | || | || ||| | || | || | | | | || || ||| || |||||| ||||| ||||||||||||||||| ||||| ||||| ||||| || || |||||||| | || || || ||
gtgaatgaatataacgaatccgccgccggcgtcatctcctcctcccacctcgactcgccttggtcgccgtcggcggccatttcgtcgccgcgcggcgagccgcccatgttgagctcgcggcggatctgatgggcttgttgtgatctcctgcagGTAAGGAAGAGGA----GGAGGGCAGGATGTCGCACCGTAAGTTCGAGCACCCGAGGCACGGCTCCCTCGGCTTCCTTCCCAGGAAGCGCTCCTCCCGCCACCG-----Mapped 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|208160552|gb|GD960458.1|GD960458EST: CCCATTCAACATTTTCTCTGTCTATCTCTCGTTGTAGCGTAGCGCAGCAG TTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACAC
genomic: CCCATTCAACATTTTCTCTGTCTATCTCTCGTTGTAGCGTAGCGCAGCAGgtatgttccc ... aatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACAC
EST:
gi|151408452|gb|EV278260.1|EV278260EST: TCGTTGTAGCGTAGCGCAGCAG TTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACAC
genomic: TCGTTGTAGCGTAGCGCAGCAGgtatgttccc ... aatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcttttcttatgaatgaatgaatgcatgcttatattttgagtgaatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
ttatattttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttcccaaccatttcctgcgttctgttctgctctgttcggttatgatagatccgttagtgttttctcttccgttttgcttttcttatgaatgaatgaatgcatgcttatattttgagtgaatttgacagTTGAATTTGGAAAACAAGATGTCTCACCGCAAGTTCGAGCACCCGAGACACGGTTCCCTTGGCTTTCTCCCAAGGAAGCGAGCTTCTCGTCATCGCGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT