Sequence
atgc intronic sequence ATGC exonic sequence...gccggcacaaattgttgtcattcatatcatctatgccctttttgtagttctaatggttttagtctgaatttaatgtctttgaatttgctttgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
Basic information
species | Glycine max |
transcript | GLYMA19G35370.3 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
gccggcacaaattgttgtcattcatatcatctatgccctttttg----tagttctaatggttttagtctgaatttaatgtctttgaatttgctttgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
| | ||||| | || | ||| |||| || |||||| | | | | | ||||| || || | | |||||| || ||||| || || ||||| || || || || ||||||||||| |||||||| || || || |||||||||||||||| | ||||| || || |
tcatgtgttaattgct--tgctccggtt-tctgtgccacttacaagctcagttcttact-tatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
gccggcacaaattgttgtcattcata-tcatctatgccctttttgtagttctaatggttttagtctgaatttaatgtctttgaatttgctttgtc-ttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
| || || || | || | | || | | | | | | || | | | | | ||||| ||| ||| | |||||||||| ||||| ||||||||||| ||||| || |||||||||||||| |||||||| |||||||| ||||||||||||||||| | ||||| || || |
aatgatttgc-ttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatca-atctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 12
gccggcacaaattg-ttgtcattcatatcatctatgccctttttgtagttctaatggttttagtctgaatttaat-gtctttgaatttgctt-tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
| | || || || | || | ||| ||| || | | || | | | | | | ||| || || || || | |||||||||||| ||||| ||||||||||| ||||| || ||||||||||| || |||||||| || ||||| |||||||||||||||| | ||||| || || |
-tcaaaataatttacttattatcctcctcaactactaatattgctcatactttgtg--tacaatgtaagtcaaattatcattttcttcatttattacttttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTG
upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
lower sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------------------------gccggcacaa-attgttgtcattcatatcatct-atgccctt---tttgtagttctaatggttttagtctgaatttaa--tgtctttgaatttgctttgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
|| ||| || | |||| | || ||| | || | || | | || | | || |||| ||| ||| | | || || || | |||||||| |||||||||||||| || || || ||||| || |||| ||||| || ||||| || ||||||||||||| | | || ||||| || |
gtaacgtctatgctccagtagttatgaatttctagaccagcagaacaatgtt-tagcagatgccattttatatcattaactatatacacttggaatatcatacaagagtttagactgtgtttttccctttctattccttcagATTTACAGAGTTTCAGATATGGAACTGGTGAGAGTACTTCCAAGCTCAGAGGATGAAGTTAATGTTGCTTGCTTTCATCCTTCTCCTGGGGGAGGTCTTG
upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------gccggcacaaattgttgtcattcata----tcatctatgccctttttgta-gttctaatggttttagtctgaa-tttaatgtctt-tgaatttgctttgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
|| || | | || | | | || | | || || | |||| ||| | | ||||| ||| | |||| | |||||| | |||| ||| |||| |||||||||||||||||||| |||||||| ||||| ||||||||||||||||| || |||||||||||||| | |||||||| || |
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------------------------gccggcacaaattgttgtcattcatatcatctatgccctttttgtagttctaatggttttagtc---tgaatttaat-------gtctttgaatttgctttgtctttta---gGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
| | || || | | | | | | | | || | || | || | | || ||| | | |||| | | || | | |||| ||||| ||| |||||||| ||||||||||| ||||| ||||| | |||||||| ||||||||||| |||||||| ||||||||||| | || || || || |
gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------------------------------------------gccggcacaaattgt-tgtcattcatatcatctatgccctttttgtagttctaatggttttagtctgaatttaatgtctttgaatttgctttgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
| | || | || || || | || ||| | | ||| ||| | | | || | | || || ||| || | || | ||||||||||||| ||||||||||| ||||| || || ||||| ||||| || ||||| || |||||||| || |||||||| | || || || || |
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattcta-cattcctacttgcgttgataactcaatcttcctggactaagcacag-gttttctctttttctgt-tcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTGMapped 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|10847791|gb|BF071604.1|BF071604EST: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG GTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
EST:
gi|193686900|gb|FK632523.1|FK632523EST: GTNTTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG GTATACAGAGTGTCAGATA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATA
EST:
gi|12690329|gb|BG156665.1|BG156665EST: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAG GTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
genomic: GTATTGTCATTGATGGAGAAACAACATTACCTATATATACAGTGTTAGAGgtaaaatgct ... tgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttctaatggttttagtctgaatttaatgtctttgaatttgctttgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
tttgctttgtctttt CT-rich tract
aatttaatgtcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccggcacaaattgttgtcattcatatcatctatgccctttttgtagttctaatggttttagtctgaatttaatgtctttgaatttgctttgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA