Sequence
atgc intronic sequence ATGC exonic sequencegtgagcatggtgttatatcattttgataaacttaatatctgtatcttggtcacatttttatgaaaagatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
Basic information
species | Glycine max |
transcript | GLYMA02G26620.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
----------------------gtgagcatggtgttatatcat--tttgataaacttaatatctgtatctt---ggtcacat------ttttatgaaa----------------agatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
| | ||| | | |||| || ||| || | | || | | || | | ||| | | |||||| | | || || ||||||||||||||||| |||||||| || ||||| | |||||||||| ||||| || || ||||| || |||||||| ||||||||||| || ||||| ||
gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT
upper sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g07080.1 (Oryza sativa), 3'ss of exon 11
---------gtgagcatggtgttatatcattt-tgataaactt---aatatctgtatcttggtcacatttttatgaaaagatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
| | || || || | || | | ||||| || ||| | || | | ||| || ||||||||||||| || ||||| || || |||| | ||||||||||| || || |||| ||||| || |||||||||||||||||||| |||||||| ||
gtttgtggtgaaactttgttgaaatgctgcctgtggtgtgttctggaatatgcaaatattgctagatttacctttgcattgtat---tttccatttcagCGGATTCGTTATCAGTGGAATCGTTGCTGGAACTTCTGGATGAGGATAGCTTACGGAAAGACACTGCGCTTCCTTCACCTGAATGGTCATCAGATCATAT
upper sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 11
------------------------------------------------------------------------------------------gtgagcatggtgttatatcattttgataaactt--aatatctgtatcttg-gtcacatttttatgaaaagatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
| | | ||| || | | | | |||| | || ||| || | || | | | || || | ||||||||||||||||| ||| ||||||||||||||| | |||||||||| || ||||| || ||||| || |||||||| ||||||||||| || ||||| ||
gttagtgcttaaattcttggactggttcaagcgcttgctctatctcttccctttactttggttcaagcgcttggccgcttgcgctatctcttttccttttagtttggctatctctgttgatctggaataagtagatattgtgttaacattgtcttttacaatgtgctcttctatttcagCGGATTCATTGACTGTAGAGTCATTATTGGAGCTGTTGGATGAGGATAGCTTGAGAAAAGACACGGCTCTTCCTTCTCCTGAATGGTCATCGGATCATAT
upper sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 10
---------gtgagcatggtgt-tatatcattttg--ataaacttaatatctgta-tcttggtcacatttttatgaaaagatatgact-tgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
| || | | || || || |||| |||| | || | || | | |||| || ||| | | ||||||||| || ||| ||||| ||||||||||| | |||||||||| ||||| || || |||||||| ||||| || |||| |||||| |||||||||||
tctgtgtttgcagcttctgtatctccatttttctggaataagattaaaggcactaattgtgcttattcttttgataatgaccatgtttgttctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT
upper sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G118467_T01 (Zea mays), 3'ss of exon 10
--------------------------------------------gtgagcatggtgttatatcattttgataaacttaatatctgtatcttggtcacatttttatgaaaagatatgact-tgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
| | || | | || || || | | || | || || | | |||| | | ||| | | |||||||||| |||||| ||||| ||||||||||| | ||||||| || || || || || |||||||| || || || ||||||||||| |||||||||||
gttggtgcatggagactcacccacgcacacagtagactttaattctatgtttgcagcttctgtatattcattttcctctaataag-attgtgcttattcttttgatgatggcgatgtttgttctctttcagCGGACTCATTGACAGTGGATTCATTATTGGAACTTTTGGATGAAGAAAGCTTAAGAAAAGACACAGCTCTCCCATCCCCTGAATGGTCATCAGATCACAT
upper sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 10
------gtgagcatggtgttatatcattttgataaacttaatatctgt----atcttgg-tcacatttttatg----aaaagatatgacttgtg----gtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
| || || | ||| | | | | | || |||| | | | |||| || || || || || || ||||||||||| | | ||||| || || ||||| | ||||||| ||| ||||||||||||||||| ||||| || || |||||||| || ||||||||
gttaacttaagtgcttactttcaggggttttacgcgcc-agtgtttgctttcatctcagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT
upper sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 10
----------------------gtgagcatggtgttatatcattttg-------ataaacttaatatctgtatcttg----gtcac--atttttatga-------aaagatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
|| |||| | || ||||| || ||| ||| |||| ||| || | || |||| || | | ||| || |||||||| |||| || || || ||||| ||||| ||||| | |||||||||| || ||||| || ||||||||||||||||| || || |||||||| ||||| ||
gtaatctttttcctacatgtcggtttgcatctttttcctatattttatttacacatgtgcttcatacttgtagtttgtgccgttattgatgtttaggattctctaataaataagatttgtggttccagCCGACTCTTTAACGGTGGAATCATTGTTGGAACTCTTGGATGAGGATAGCTTGAGAAAAGACACAGCACTTCCTTCTCCGGAGTGGTCCTCTGATCATATMapped 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|6481835|gb|AW201106.1|AW201106EST: AAATGTCACTAGAGATTTTATTGGCACTCTAGATTACATATTTTACACAG CGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTT
genomic: AAATGTCACTAGAGATTTTATTGGCACTCTAGATTACATATTTTACACAGgtgagcatgg ... gtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatatctgtatcttggtcacatttttatgaaaagatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
acttaat putative branch site (score: 4)
atttttatgaaaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcatggtgttatatcattttgataaacttaatatctgtatcttggtcacatttttatgaaaagatatgacttgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA