Sequence
atgc intronic sequence ATGC exonic sequencegttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagttattttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
Basic information
species | Glycine max |
transcript | GLYMA07G11560.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 2
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagttattttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
| || ||| | | ||| ||| ||| | | ||| || || | | | | ||| ||| | |||| | ||||| | || | | || ||| ||||| ||||| || ||||| ||||| ||||| |||||||| || |||||||| |||||||| ||||| |||||||||||||| ||||| |
---------caaagaaaaatcttgtatgtgtgcttaagt----tcaaaatctcgtaaagaaaaaatgtatgtacacccgtttgcttattctggttttgtg---tgatttactttagAAATC---GGACTTGGAGAAGGCGCAGCTTGGCCTGGGTCATAGCTACAGCAGGGCGAAGGTGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGG
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagttatt--ttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
| || || ||| || | || ||| ||| | | ||| | |||||| || |||| | | ||| | | ||||| || | || ||||||||||| || || || ||||||||||| || ||||| |||||||| || |||||||| |||||||| || |||||||| |||||||
-----------tgttggactgcaatgctttgatgctttcatatgttcc---ttgcataaaatggtttttttcctgttattgtttgtttacttgctcctttgttttcgattg-------cagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G110233_T01 (Zea mays), 3'ss of exon 2
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaag-ttattttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
| | || | ||| | | || || ||||||| || | | | | ||| ||| | | || | | ||||||| | | | || | | ||||| ||||| |||||||| ||||||||||| |||||||| || |||||||| |||||||| || |||||||| |||||||| || ||||
---------tgatgagcttacgcattgctttttatatgcctaaat----tgttgtaaagctaaacgcctgctgtgcttaatttggctttaccatgtgtccatgttgattgta----gGATTCTG---ACTTGGAGAAGGCCCAACTTGGCCTGGGGCATAGCTACAGCAGGGCTAAGGTGAAGTTCAATGTGAATCGTGTTGATAACATGGTGATCCAAG
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 2
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagttattttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
| | || || || | || |||| | | |||||| || || || | |||| || ||||| ||| | | ||||| || ||||| ||||| || ||||| ||||||||||| |||||||| || |||||||| |||||||| || ||||||||||||||||| || || |
-----tgcaaaattttggctgctgggcttatgcatagtgtatcaaattttgttgtgaagttggatgcttgatg--------tgcttaatttgtttttcc-----gatggtgat-tgtagGATTCTGACTTGGAGAAGGCCCAGCTTGGCCTGGGGCATAGCTACAGCAGGGCCAAGGTGAAGTTCAATGTGAATCGTGTTGACAACATGGTGATCCAGG
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagttattttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
| | ||||| || ||||||| | |||| ||| | | | ||| | || | || | || | ||| | | || ||||| | || ||| | ||||| | || ||||| | | || || ||||||||||| |||||||| |||||||||||||| || || |||||||| |||||||
----gtgtgatctcctttct-atgtgttt----------aaaatctttttgtc-tgtttgcttatctcatatggtttgtgttctcataaaaaatttctgt-----------ttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagttattttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
|||||||||| | || ||| | | || |||| ||| || | | | | | || || || ||| || ||||| | || ||||||||||| || |||||||| || | ||||| |||||||||||||||||||| |||||||||||||| || || |||||||| |||||||
---------------------gtgtgtttttt---atttttgattacc-taatacctacacatat-ttttgctattcgtgct--caatatcatcttcttt----------ataatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagt------tattttatttaaattatttttttt--ccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
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------gtttgctt-tatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGGMapped 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|207807220|gb|GD779319.1|GD779319EST: TGTGCGCCTCCATTTTGATAGGTTTGTCAGTGATCTCAAG TCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGA
genomic: TGTGCGCCTCCATTTTGATAGGTTTGTCAGTGATCTCAAGgttagcattt ... aattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttcgcaagttattttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
ccttgat putative branch site (score: 5)
ttattttatttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagttattttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG