Sequence
atgc intronic sequence ATGC exonic sequence...ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
Basic information
species | Glycine max |
transcript | GLYMA10G02410.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 23
ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
|| | | | ||| || ||| | | || ||| | || || | | || | || || || |||||||||||||||||| ||||||| | || ||||| || |||||||| || ||||| || ||||| || ||||| ||||| ||||||||||| || || || |
-------gtatgcttgagcat-gtgggttggttttattgtcattagtgatttatttggtcacggt-----atgatccatacaaaatgcaacatttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAAAACGAATTTATGGTGAATTGGGATGGATTACGCACTA
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 23
------ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
|| | | |||| | | ||||| | | || | || || |||| | | | | | || || | |||||| |||||||| | ||||| || || |||||||| ||||| || ||||| || |||||||||||||| ||||| || ||||| || ||||||||| | ||||||
gtaagtaaattgtaattgatcaatcacaacgcctttct---gaattccctgtg---atgtttgctttctagtttatcttcttcatct--tgtgttgt-----atagGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATGCGTAAAATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatct-gtgtttgatttgctgt--gttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
| || || | | || || | | || ||| | || | || |||| | | || | | | || || | || | | | |||||||| | ||| | || ||| | || || || || || ||||| |||||||| || ||||| ||||| || ||||| |||||||||||| || ||||||
-tgtgaatcactcttttttatattgcctatgatt--cagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
||| ||| | ||| |||| ||| | |||| | | | | ||| | | | | |||| || ||| ||||| ||||||||| ||||||| | |||||||| || |||||||| || ||||| || |||||||||||||| ||||| ||||||||||| ||||| || |
---------gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaacttttttt--ttgactttctg------------cagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 3
ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaa-ttatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
||| ||| | ||| |||| ||| |||| | | | | ||| || | | | ||||| || ||| ||||| ||||||||| ||||||| | |||||||| || |||||||| || ||||| || |||||||||||||| ||||| ||||||||||| |||| || |
---------gtatgcaagcacacaagtttactttagtaatcactaccggcacagtatataccaacttctttttttttgactttctg------------cagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCACACTA
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 14
ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
||| ||| | || | || ||| || | || ||| | | | |||| ||||| || ||| ||||| ||||||||| ||||||| | |||||||| || |||||||| || ||||| || |||||||||||||| ||||| ||||||||||| |||| || |
---------gtatgcaag-cagacaggttacattagtaaacactgttggtac----agtgtacaccaactgtctttgactttctg------------cagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 2
ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
||| ||| | ||| |||| ||| | |||| | | | | ||| | ||| | ||||| || ||| |||| ||||||||| ||||||| | |||||||| || |||||||| || |||| || |||||||||||||| ||||| ||||||||||| ||||| || |
---------gtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaact-tctttttttgactttctgg------------agGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCACAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
ggcttaaacatatt--caaatctagtgtttttctttggtagct-tctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
| | || || | | | | || | || || | || ||| | || | | | ||| | | | | ||| |||||||||| ||| | ||||||||||| ||||| || || ||||| ||||||||||| |||||||| ||||||||| | || ||||| || || || ||||
--atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatg-tagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
ggcttaaacatattcaaatctagtgtttttctttggtagct-tctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
| | | | | | || | || || | || ||| | || | | | ||| | | | | ||| |||||||||| ||| | ||||||||||| ||||| || || ||||| ||||||||||| |||||||| ||||||||| | || ||||| || || || ||||
-----gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatg-tagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 22
---ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatgg--cagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
| || || ||||| ||| | | | | | | | | | | |||| | | | | ||| | |||| | | | || ||||||||||| ||||| || |||||||||||||| || || ||||| ||||||||||| |||||||| || |||||||| || ||||||||||| ||||||
gtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATGCGTAAGATGAAGAACGAGTTCATGGTAAACTGGGATGGTTTAAGAACAA
upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 22
---------------------------------------------------------------------------------ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttc------aattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
| | ||| | ||||| || | || | | | | || ||||| |||| || || | | || | || | ||| || | |||||||| || |||||||| |||||||||||||| || || ||||| |||||| | |||||||||||||| |||||||| || |||||||| | || ||||
gtaagttgaataaatctttaaattcatccacaacttttgctataatgttcctcactctttttatgggtccatggatttagtgacggtaac-tgttcaatccttttaattcgccattctgatctttagtttctttcttcttttcctgttaaaaaatttattgttaactta--gatttattgttt-cagGTTGACAGCATGTTAGGGAGACGTGAAAATCCAGGAGAACATGAAGCTATGAGGAAAATGAAGAATGAGTTCATGGTGAACTGGGATGGCCTACGTACAAMapped 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|193601240|gb|FK552625.1|FK552625EST: TCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG GTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATG
genomic: TCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAGgttggtataa ... ctgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
tactgat putative branch site (score: 2)
ttagtttcaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - gcttcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctgt