Sequence
atgc intronic sequence ATGC exonic sequencegtatgcattcttttgatttttttcaatcttgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaagaacattgactgtgagattataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
Basic information
species | Glycine max |
transcript | GLYMA14G40570.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
--------gtatgcattcttttgatttttttcaatct-tgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaagaac-------attgactgtgagat-tataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
| ||| || |||| | |||| | ||||| |||| || || || | ||| || | | | || || |||| | | | | | |||| |||||||||||| |||||||||||||| |||||||||||||| || |||||||| || ||||| |||
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatc---aaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
upper sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 4
----------------------gtatgcattcttttgatttttttcaatcttgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaaga-acattgactgtgagattataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
| ||| ||||| | || ||| | | || ||| ||| | | |||| | | |||| | | |||| | | | ||| | |||| ||||||||||| |||||||| ||||| |||| |||||||||||||| || || | ||||| |||
gtatgcccactcctttgcttctcggtttatttagttgatatcttggcttctctgcctcctagtaccaaaatttag-gttccctgtattttcccccttccacaatagtttgaatttcatattt--gtttgcagGCTAATCCAGACTACAAGGGTGTCTGCCACATTGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG
upper sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgcattcttttgatttttttcaatcttgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaagaacattgactgtgagattataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
| | | | ||| ||| || || ||||| | | | || || || | || | | | ||| ||||| ||||| || ||||||||||||||||| ||||| || ||||||||||| ||||||||||||
-----------------gtatgatggtttgaattgattctgttttgctt-------gcatt----cggatgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
upper sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 4
gtatgcattcttttgatttttttcaatcttgatttgt--tcgtttca--actcttaaagagcattgtaatgcacaatgtccaagaacattgactgtgagatt-----ataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
||||| |||| | ||| | || ||| || | | | | | | || | || | | |||| || ||| | || || | | ||||| || ||||| ||||| ||||| ||||||||||||||||| || ||||||||||| ||||| ||||||
gtatgatgcctttcaggtgtttcatgttttagtttccaaccgctaaactatcttgctaaaaggttatcatctgtccttgtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
upper sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 4
gtatgcattcttttgatttt----tttcaatcttgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaagaacattgactgtgagatt-----ataaa-atacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
|||||| ||| | | ||| ||| | | | | | | | | | ||| | | || | | | || ||| ||| | || || | || |||| ||||| || || || ||||| ||||||||||| ||||| || ||||||||||| ||||| ||||||
gtatgc-ctctctggtctttcatgttttagtttccaaccactgaactatattgctgaaggtg--tatcatctattcttgtttattgcactgaatgtaaactttacgtatgagcatgcagGCCAATCCGGATTACAAAGGTGTATGCCATGTTGCCCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG
upper sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgcattcttttgatttttttcaatcttgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaag--aacattgactgtgagattataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
||| | | | | | | || || |||| || || ||| | ||||| | | || | | | || | |||| |||||||| || ||||| ||||||||||| |||||||| ||||| || |||||| | || ||||||
------attatgtaaaacggatcacacatggaggcattattttcttctattctcac---ttgatacgcacagtaattgatttaatgctaattttgtcgaacttg--cgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG
upper sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16666 (Selaginella moellendorffii), 3'ss of exon 3
gtatgcattcttttgatttttttcaatcttgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaagaacattgactgtgagattataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
| ||| || | | | | | || || |||| |||||| ||||| |||||||||||||| |||||||||||||| |||||||| || | || || |||
-----------------------------------------------------gtacgtttgcggtgtttg-tatgtgattctgtcgctctaacccggatttgatgcagGCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAG
upper sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16664 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcattcttttgatttttttcaatcttgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaagaacattgactgtgagattataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
| || ||| || || | | | | || || | || |||| |||||| ||||| |||||||||||||| ||||||||||||||||||||||| || || || || |||
------------------------------------------------gtacgtttgcggtgtt-tgtacgtgattcggtcgctctaacccgga-----tttgatgcagGCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAGGAAGGTCACTGCAGTCCGGGCGAG
upper sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 3
gtatgcattcttttgatttttttcaatcttgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaagaacattgactgtgagattataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
| || ||| || || | | | | || || | || |||| ||||| ||||| |||||||||||||| |||||||||||||| |||||||| || | || || |||
------------------------------------------------gtacgtttgcggtgtt-tgtacgtgattctgtcgctctaacccgga-----tttgatgcagGCGAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAGMapped 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|209702338|gb|BW656311.1|BW656311EST: AGCAGAATATCAAGTACTTTTATGATATTAAGGATCTTAGTAATTTTAAG GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGT
genomic: AGCAGAATATCAAGTACTTTTATGATATTAAGGATCTTAGTAATTTTAAGgtatgcattc ... taaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagcattgtaatgcacaatgtccaagaacattgactgtgagattataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
cattgac putative branch site (score: 3)
tgagattataaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcattcttttgatttttttcaatcttgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaagaacattgactgtgagattataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA