Sequence
atgc intronic sequence ATGC exonic sequencegtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
Basic information
species | Glycine max |
transcript | GLYMA14G06340.2 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
gtaggatgaatattggcaaaaatttcattaga-tatcagttgttgcatgccataacactaatgggaaatttcattgatatgc-tatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
|| | | ||| | || ||| | |||||||| | || || | | || ||| ||| ||| || |||||||||| | | |||||||||||| || ||| |||||||||| ||||||||||| |||||||| |||||||| ||||||||| | ||||| || ||||
gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattt-tgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
gtaggatgaatattggcaaaaatttcattaga-tatcagttgttgcatgccataacactaatgggaaatttcattgatatgc-tatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
|| | | ||| | || ||| | |||||||| | | || | | || |||||||| | | || |||||||||| | | |||||||||||| || ||| |||||||||| ||||||||||| |||||||| |||||| | ||||||||| | ||||| || ||||
gtttgtttcttatggcagggccttctattggtctatcagttttgctccgtttcaaaattt-tgaactatttcattattctttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
-----------gtaggatgaatattggcaaaaatttcattagatatcagt--tgttgca-tgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
| | | |||| | | || ||| || |||| || | || | || ||| || | | ||| | | | |||||||||| | | |||||||||||| |||||| |||||||||| || |||||||||||||| || |||||||| ||||||||| | |||||||| ||||
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgat-tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
-gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatg-----ggaaatttcattgatatgct---------atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
||| || || | | ||||| |||| | | | | ||| | | ||| |||| | | || || | | |||||||||| | | |||||||||||| |||||| |||||||||| || || ||||| |||||||| |||||||| ||||||||| | ||||| || ||||
gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 2
--------------gtaggatgaata--ttggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgct----atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
| | | | | || || | || || | | ||| | || || | | | || | || ||| | || | |||||||||| | | |||||||||||| |||||| |||||||||| || |||||||| |||||||| |||||||| ||||| || | ||||| || ||||
gttagcatctgaatgaaaatttatttccttagcgcactttggatagaagccctgttttcaaattccttcccccaaaatctgacttgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCTGTGAATGAAGCCTTGAACGAACTTTATGTTGAAGAGG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
---------gtaggatgaatattggcaaaaatttcatt--agatatcagt--tgttgca-tgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
| || | || | | || || | ||| || |||| || | || | || ||| || | | ||| | | | |||||||||| | | |||||||||||| |||||| |||||||||| || |||||||| ||||| || |||||||| |||||||| | |||||||| || |
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgat-tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
|||| | | | | || ||| ||| || ||| ||| || || || | | ||| | | | |||||||||| | | |||||||||||| |||||| |||||||||| || |||||||| ||||| || |||||||| |||||||| | |||||||| || |
gtagtgc-actttgaatagaagccctatt-----tcaattc---catcccaaaaatctgat------tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 9
gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
|||| | | | | || ||| ||| || ||| ||| || || || | | ||| | | | |||||||||| | | |||||||||||| |||||| |||||||||| || |||||||| ||||| | |||||||| |||||||| | |||||||| || |
gtagtgc-actttgaatagaagccctatt-----tcaattc---catcccaaaaatctgat------tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCATGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
-----------gtaggatgaatattggcaaaaatttcattagatatcagt--tgttgcatgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG-----------------------------------------------------------------------
| | | |||| | | || ||| || |||| || | | || ||| || | | ||| | | | |||||||||| | | |||||||||||| |||||| ||||| |||| || |||||||| ||||| | |||| ||| ||||||||| | |||||| ||||
gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgat-tcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
gtaggatgaatattggcaaaa--atttcattagatatcagttgttgcatgccataacactaatgggaaatttcat-tgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
|| || | | || | ||| || ||| | || ||| || ||| |||| | |||| | ||||||||||| | |||||| | || || || |||||||||||||| ||||||||||| |||||||||||||| || ||||||||||||| || || || |
gttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattac-ttaacaattggtttcttctgatct----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
---gtaggatgaatattggc--aaaaatttc-attaga----tatcagttgttgcatgcca---taacactaatgggaaatttcattgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
||| ||| |||| || | |||| ||| | ||||| || || | || || || ||| | || | ||||||||||| | || ||| | || || |||||| |||||||||| ||||| |||||||||||||| |||||||| ||||||||||||||| || || |
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAGMapped 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|298199409|gb|HO042772.1|HO042772EST: TCCTTGCACTTCATGTGGACCATGCACGTGTTGTTGACGTCATGCGGAAG GCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGC
genomic: TCCTTGCACTTCGTGTGGACCATGCACGTGTTGTTGACATCATGCGGAAGgtaggatgaa ... tatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGC
EST:
gi|208310285|gb|GE105533.1|GE105533EST: TCCTTGCACTTCACGTGGACCATGCACGTGTTGTTGACATCATGCGGAAG GCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAAC
genomic: TCCTTGCACTTCGTGTGGACCATGCACGTGTTGTTGACATCATGCGGAAGgtaggatgaa ... tatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatcagttgttgcatgccataacactaatgggaaatttcattgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
aaatttcattgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG