Sequence
atgc intronic sequence ATGC exonic sequence...tgatatcattttggggttcacttggaaggcattgcatggtggtacttcaattgcagatgtagagtatgctttgtgctgagtttcctgttcttctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG
Basic information
species | Glycine max |
transcript | GLYMA09G39770.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 10
-tgatatcattttggggttcacttggaaggcattgcatggtggtacttcaattgcagatgtagagtatgctttgtgctgagtttcctgttcttcttta-cagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG
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actgcacatttatagcccttgttgcctgtgtgct-cattctgctctctagaatttgattata-actgttcgatttgtaagttatcctttttatgttgaacagTTGCTTCGTCCAATTTACAAGCAAATTGCTGAAAATAGGAACGCTGAGATATTTTCAGCAAATACTCTCCTTGTTATTTTTGGAACAAGTCTTCTCACAG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 9
------------------------------------------------------------------------------------tgatatcattttggggttcacttggaaggcattgcatggtggtacttcaattgcagatgta--gagtatgc---tttgtgctgagt--ttcctgttcttcttt--acagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG
|| || ||| | | | | |||| || | || |||||| || | | | ||| | ||| |||| || | || | | |||| | ||||| || || |||||||| |||| |||||||| ||||| || || || ||||| |||||||||||||||||| |||||||||||||||||||||
gtgagtttactgttcatttacattattttccctatcctttctgggactttttttgtgtgccatatgtagactctaggctcagctggacatgggcttgtttctttgcttgcatgcatgtttcagttttttctcc-ttgcagctgaatttaatctgcaactatgtaatgagcaatttccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------------------------------------------------------------tgatatcattttggggttca-cttggaaggcattgca--tggtggtacttcaattgcagatgtagagtatgctttgtgctgagtttcctgttcttctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG
| || | | |||| || | ||||| || ||| |||||| | | ||| ||||| | |||| | || | |||| | || || || || ||||| || |||| |||||||| ||||| || || || ||||| |||||||||||||||||| |||||||||||||||||||||
gtgagttgactgttcatttacattattttgcttatcctttctggtactttttgtatgccatacgtagactctgggcccagctggacataggtttggttccttgcatacatgcatgtttcagtttttttccccttgcagctgcatgtatctcaattatctaca---actatttaatgtgc-aattttcgttttgtatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 10
tgatatcattttggggttcacttggaaggcattgca--tggtggtacttcaattgcagat----gtagagtatgctttgtgctgagtttcc--tgttcttctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG
|||| ||| ||| | || ||| | |||||| | || | | | |||| | | | || ||| | | || || || |||| ||||||||||| |||||||| |||||||||||| ||| || || || ||||| ||||| || || || ||||||||||| || ||| | || ||||
-----tcatg--aaagttaactgtgctatcactgctacttccggtactcaatttatatgtttcaatggagt-tataatataaggaatttacactcttgttgcatatagCTTCTTCGACCAATCTACAAGCAAATTGCAGAAAATCGAAACGCCGAGATATTCTCTGCCAACACGCTTCTCGTTATTCTTGGGACTAGTTTACTGACAG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
--tgatatcattttggggttcacttggaaggcattgc--atggtggtacttcaattgcagatgtagagtatgctttgtgctgagtttcctgttcttctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG
|| | | | | | | || || ||| || | || | | || | | | || ||| |||| || | |||||| || || || ||||||||||| |||||||||| | |||||| || || ||||| ||||||||||| || ||||||||||| || ||| | |||||||
aatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgctgaatcatagttttacaatgcattgattttctggtacac----acagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
tgatatcattttggggttcac-ttggaaggcattgcatggtggtacttcaattgc------agatgtagagtatgctttgtgctgagtttcctgttctt--ctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG
||| | | || | | ||| | | ||||| || | | || | | ||| || | ||| || | ||| ||||| ||| ||||||| || ||||| |||| ||||||||||||||||| || || || ||||||||||| |||||||| | || || ||||| |||||||
---------attgagacttgtgttacagcatctgatatgtttctccttcagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAGMapped 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|16996864|gb|BM086236.1|BM086236EST: CTGTTAAGGCAGCAGTTGCCATCACTGCTATAATTGCAGGGGGACGTTTG CTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCTGAAATT
genomic: CTGTTAAGGCAGCAGTTGCCATCACTGCTATAATTGCAGGGGGACGTTTGgtaagtggtt ... ttctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaattgcagatgtagagtatgctttgtgctgagtttcctgttcttctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG
tttcctgttcttcttt CT-rich tract
ttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatatcattttggggttcacttggaaggcattgcatggtggtacttcaattgcagatgtagagtatgctttgtgctgagtttcctgttcttctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG
- - - - - -tggggtt
- - - - - - - - - - - tggaagg
- - - - - - - - - - - - - - - - -gcatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - gcagatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgctg