Sequence
atgc intronic sequence ATGC exonic sequencegtaaatctgagcttcatgaagtggagttgcttcttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
Basic information
species | Glycine max |
transcript | GLYMA12G08080.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g01890.2 (Oryza sativa), 3'ss of exon 4
--------gtaaatctgagcttcatgaagtggagttgcttct--------tttgtggtgaagttttactcaaatttgtttttctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
|| |||||| | | | || || || | | || | | | | | | | || | || || | || || ||||| |||||||||||||| || |||||||||||||| ||||||||||| || || ||| | |||||||||||||||||||||||||||
gtaagtaaatagttctgagtgac-tcaggtagaattattgttggatggacttgctctttcgatatcatgctatcttaactgccttttatc-ttgttctagGCTCCTTTCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACTGGTACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 3
------------------gtaaatctgagcttcatgaagt--ggagttgct-tcttttgtggtgaagttttactcaaatttgtt---tttctgttgcgatccttg--cagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
| | | | | || | | | | || ||| | | | || |||| | ||| | | | | ||| ||| ||||||||| ||||||| ||||| || ||||||||||||| || ||||||||||| |||||||| |||||||| | |||||||||||||||
gttagtgaaatttcctttgaatgttttggttttgggcaattggaagcggctgccctctagggattggtttgccattttcttgataaactagttatatgatttttgtccagACTCCTTACAATTGCGGAGGAGACCCTGACAGAGTTCCTCTCCAAGGCTACAGGGACTGCTGTTGATTGGGTGCCAATGCCTGGGATGAAG
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G469551_T02 (Zea mays), 3'ss of exon 4
-----------gtaaatctgagctt--catgaagtggagttgcttcttttgtggtgaa-------gttttactcaaatttgttttt---ctgttgcgatccttg---cagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
||||| | |||||| |||| | |||| | ||| | || || | | | | || | | | || | | ||| ||| ||||| ||||||||||||| || |||||||||||||| |||||||||||||| |||||| | |||||||||||||||||||||||||||
gtaagtaaactgtaaaccagagcttgctgtgaaactctctcacttcaatagtgtttaataagaacgtactgttgatacatgatactaaaccttttccacttttgggccagGCTCCTTGCAATTGCAGAGGAGACCTTGACAGAGTTCCTCTCAAAGGCTACAGGGACTGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G109987_T01 (Zea mays), 3'ss of exon 4
--------gtaaatctgagcttcatgaagtgga-----gttgctt--cttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttg---cagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
| | |||| | || || ||| ||||| | | || | | || | ||| | | | || | || |||| ||||||||| | ||||||||||| || || ||||||||||| ||||||||||| || || ||| | |||||||||||||||||||||||||||
gtaagtgaatcattctggccatctggagaaggattcttgttgcgtaaccttgccatttcaagactatcctaatc-ataataccattccaattcttgtttcagACTCCTTGCGATTGCAGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 4
--------gtaaatctgagcttcatgaagtgga-----gttgc-ttcttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttg---cagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
| |||| | || || ||| ||||| | ||| | || | | || | | | | || | | |||| ||||||||| | ||||| ||||| || || ||||||||||| ||||||||||| || || ||| | |||||||||||||||||||||||||||
gtaagtgaatcgttctggccatctggagaaggatttttgttgcgtaaccttgccattgagactgtcctaa--tcatagtgccatttcaaatcttgtttcagACTCCTTGCGATTGCGGAGGAGACCTTCACAGAGTTCCTCTCAAAGGCTACTGGGACAGCTATTGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaatctgagcttcatgaagtggagttgcttcttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
||||| | || | || ||| | | ||| | | |||| || | || | ||| | || | ||| | || ||||| |||||||| |||||| |||||||||| || |||||||||||||||||||| |||||||| ||||||||||||||||||
gtaaagtttcatttttggttttgaagtaacctttttc-taatc--ttttttctttgcctaattgcttggttttggtctt---agATTGCTCTCAATCGCAGAGGAGACTTTGGCAGAGTTCCTATCCAAGGCTACAGGAACTGCTGTTGATTGGGTTCAGATGCCTGGGATGAAG
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 3
------gtaaatctgagcttcatgaagtggagttgcttcttttgtg-gtgaagttttactcaaatttgtttttctg----ttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
||| | || ||| | ||| || | | || | | | | |||| | | || | | | |||||||||||| || ||||||||||| |||||| |||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||
gtaatgtctaatacaaatgtccatcagttctctggctatttctctacatgtggatccattgtaattcagtggtatgatttctttgctttttgcagACTCCTCTCCATTGCAGAGGAGACTTTGGCAGAGTTCCTCTCAAAGGCTACAGGAACTGCTGTCGATTGGGTCCAGATGCCTGGGATGAAG
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ26528 (Selaginella moellendorffii), 3'ss of exon 3
gtaaatctgagcttcatgaagtggagttgcttcttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
||| | ||| | || |||| || |||||| || || ||||||||| | ||||||||||| ||||||| || ||| ||||||| ||||||||||| || || ||| ||||||| ||||||||||||
--------------------gtgagaatacttggaaaaagctggtcgtttatctcaaggtgtttt---gtctcg---tttgcagACTGTTGAGCATTGCAGAGGAGACTTTGAACTCATTTCTTGCAAAGGCAACAGGAACTGCGGTGGACTGGATCCAGATTCCTGGGATGAAG
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ38766 (Selaginella moellendorffii), 3'ss of exon 3
gtaaatctgagcttcatgaagtggagttgctt-cttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
| | | | |||| |||| ||| |||| || | | | | || || |||| | |||||||| | | ||||| ||||||||| |||| ||||| || ||||||||| ||| || || || |||||| ||||| ||||||||||||||
---------------gtcagtcagcgatgctcgctttcgtga--aagtgata-tgacactgaccttgcttttgc---tttggcagACTCTTGGCTATTGCGGAGGAAACTCTGACTGAGTTTCTAGCAAAGGCTAGAGGCACGGCCGTGGATTGGATCCAGTTGCCTGGGATGAAG
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ14784 (Selaginella moellendorffii), 3'ss of exon 3
gtaaatctgagcttcatgaagtggagttgcttcttttgtggtgaagttttactcaaatttgtttt-tctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG------
||| | ||| | || |||| | |||||| |||| | ||||||||| | ||||||||||| ||||||| || ||| ||||||| ||||||||||| || || ||| ||||||| ||||||||||||
--------------------gtgagaatacttggaaaaagctggtcgtttatctcgaggtgttttgtctggt-------ttgcagACTGTTGAGCATTGCAGAGGAGACTTTGAACTCATTTCTTGCAAAGGCAACAGGAACTGCGGTGGACTGGATCCAGATTCCTGGGATGAAGGCATGC
upper sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ29546 (Selaginella moellendorffii), 3'ss of exon 3
gtaaatctgagcttcatgaagtggagttgcttcttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
| | | | |||| ||| | |||| || | | | | | || || |||| | |||||||| | | ||||| ||||||||| |||| ||||| || ||||||||| ||| || || || |||||| ||||| ||||||||||||||
---------------gtcagtcagcgatgctcgctttcctg-aaagtgata-tgacactgatcttgcttttgc---tttggcagACTCTTGGCTATTGCGGAGGAAACTCTGACTGAGTTTCTAGCAAAGGCTAGAGGCACGGCCGTGGATTGGATCCAGTTGCCTGGGATGAAGMapped 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|24136783|gb|BU927293.1|BU927293EST: GTGGTTACCACTCCTCAGCATACCATGAGAGATGCTAATAACCCTGCTGG ACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTAC
genomic: GTGGTTACCACTCCTCAGCATACCATGAGAGATGCTAATAACCCTGCTGGgtaaatctga ... atccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
tccttgc CT-rich tract
ttttactcaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatctgagcttcatgaagtggagttgcttcttttgtggtgaagttttactcaaatttgtttttctgttgcgatccttgcagACTCCTATCAATTGCAGAGGAAACTTTGACAGAGTTCCTTTCAAAGGCTACAGGAACTGCTGTAGATTGGGTCCAGATGCCTGGGATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG