Sequence
atgc intronic sequence ATGC exonic sequencegtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
Basic information
species | Glycine max |
transcript | GLYMA14G06340.1 |
intron # | 20 |
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 20
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
gtaatt-ctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgta-tttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
||| || || | | | | | || ||||| ||| |||| | | ||| | ||| | | | | |||| | | ||| ||| | | ||||||||||| || || || || || ||||| || ||||| |||| ||||| || ||||| || ||||||||||| || ||||| || ||||||||||||
gtagttactcttactcctgatg----ttggtatttcttaaggtggcataccttaat--attaa---atttctcaacatggcatgcattgatattaaattttctttatattc----atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
| || | || |||| || | | | | |||| | | | || | |||| || | || || | | ||||| |||| | || | |||||||||||||| || || || ||||||||||| ||||| || |||||||||||||| ||||||||||||||||| || ||||| || || |||||||||
--------gtgatatagataaaa--tctgatctcgtttctgtaaacaagcacgattctt----gtattt----atatgcttatgtttaca-atgtttctctc-----tgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
|||||| | ||| | | | || | | | |||| | | | | | | | | | ||| || | |||| | | ||||| | ||| ||||||||||||| |||||||| |||||||| || ||||| || |||||||||||||| |||||||||||||||||||| ||||| || || || ||||||
gtaattttatca---------agatcctgctgtcattcctgtaaacaagcaccatgcagcaatttgtatttttatgacttac----aatgtct-tccctctgtgtgata-------gTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 20
gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctc-attttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
|||||| || | | | || ||||| ||||| | ||| || || | ||||| | ||| || || ||||| || |||| |||||||||||||||||||||||||||||| ||||| ||||| || || || || ||||| ||||| |||||||||||||||||||| |||||||||| |||||||||
gtaatttgtttagt--aaggaagaactttgctttctttaggtgcggtacatccaacttattttgtgattttcatatcgttttcttttg------gttc-----------atggaacagTGAGGATCCTGACATTCACTTCAAGTATATTGAAGCTGCTGCTAAAACTGGACAAATTAAGGAGGTTGAGCGTGTGACTCGAGAATCAAACTTCTATGAT
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
------------------------------gtaattctttcatttggaaaaaaaacttgtttttctgt---tggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataa----------tatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
| || ||| | || || |||| | || ||||| | || | |||| | | ||| | || ||| ||| | ||| | | ||| | || ||| ||||| ||||| || |||| |||||||||||||| |||||||||||||| ||||||||||| || || ||||| |||||||| || || |||||| |
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgc--atgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCTMapped 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|208315625|gb|GE117789.1|GE117789EST: AGGTCATATGAGGGACTGTAC-TTTTCCTTGGATCATACTTGAGCTCCAG TGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGG
genomic: AGGTCATATGAGGGACTGTACTTTTTCCTTGGATCATACTTGAGCTCCAGgtaattcttt ... tatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
ctctaaa putative branch site (score: 3)
taaataatatggaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA