Sequence
atgc intronic sequence ATGC exonic sequencegtatttgcaatttcgtatggtgtttccctctccaagtatgccagccttaataatgtaatttcttatatttggttttggtatcatcatcacctctcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
Basic information
species | Glycine max |
transcript | GLYMA05G34560.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G008556_T01 (Zea mays), 3'ss of exon 5
----------------------------gtatttgcaatttcgtatggtgtttccctctccaagtatgccagc-cttaataatgtaat-ttcttatatttggttttggtatcatcatcacctc---tcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
| | || || || | | || || | |||| || | || |||| || | || ||| || || | | | |||||||||||||||| || ||||| ||||| | | ||| | ||||| ||||||||||| | |||||| |||||||| | ||||||||||| ||| ||
gtaagtgggtgcatgcagtttattctctatcatgaaaacacaataacttggcattccaattgaatagtttagtgcctaattgattattattattattattattattattattattattattttgcattgcagGAAGAAAATAAAATCTTAGACAAGCTGCATCGCCAAAAGATTGCAGAAGTTGAAAAGCTGAGCCAAACTGTGAGAGAGTTGGAAGAGGCTGTTCTTCAAG
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatttgcaatttcgtatggtgtttccctctccaagtatgccagccttaataatgtaatttcttatatttggttttggtatcatcatcacctctcc----tagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
|||| || ||||| | | || ||| | ||| ||| || ||| | | || || | | ||| | | | |||||||| || | |||||||||||| |||| |||| ||||| ||||| ||||||||| ||||||| ||||| | || || ||||| ||||| ||||| |
gtat---cactttcgcctcct-ttacccagcagtactataaattcctggatctctctccttcgttttcgtgagcatgccttgtttatcgattgttcaaattagGAAGAGAACAGAATTTTGGACAAGTTGCACAGACAAAAGGTTGCAGAAGTTGAAAAGTTTACCCAGACCGTACGGGAGCTTGAAGAAGCTGTTCTTGCTG
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatttgcaatttcgtatggtgtttccctctccaagtatgccagccttaataatgtaatttcttatatttggttttggtatcatcatcacctctcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
| | |||| || | | | | | ||| | || | | | | | || | | | || || | ||||||||||| |||||| | || | ||||||||| | |||||| || || || ||||||||||| || || || |||| |||||||||||||| |||||||
-----------gttctgtggtcgccatcttgttctttgtatttacttaatctatggatttgccaacaatctgatt----aactttattttctgttttagGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 5
----gtatttgcaatttcgtatg-gtgtttccctctccaagtatgccagccttaataatgtaatttcttatatttggttttggtatcat--catcacctctcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
|| | | ||||| | | | || | | || | | | | | | | | | || | | ||| | |||||||| |||| |||| | ||||| ||||| |||| |||||| ||||| ||||||||||||| || | || | ||| ||||||| ||||| ||||| |
gtatgtctatatcatttcttttacatattggaacaccagaatagggtatctcttccttttcttaccactgtggtggccttatttgttgatacattggttaaaatagGAAGAGAATAGAATTATAGACAAGATGCACAGACAGAAGGTTGCAGAAGTTGAAAAGCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTG
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------gtatttgcaattt----cgtatggtgtttccctctccaagtatgccagccttaataatgtaat-ttcttatatttggtt--------ttggtatc----atcatcacctctcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
| | | || || | ||| | ||| | | | | || | |||||| ||| | | ||| || || ||| ||| | | | |||||||||||||||||||||||| || |||||| | | ||||| |||||||||||||| || |||||||| || || || || ||||||||||| || || |
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTGMapped 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|208185207|gb|GD983387.1|GD983387EST: TCTCCAAAATAAAAAATCAAGAGCTAATTAAACAGATTGAGATTTGCCAG GAAGAAAATAAAATTTT
genomic: TCTCCAAAAT-AAAAATCAAGAGCTAATTAAACAGATTGAGATTTGCCAGgtatttgcaa ... cctctcctagGAAGAAAATAAAATTTT
EST:
gi|193700394|gb|FK636353.1|FK636353EST: TCTCCAAAATAAAAATACAAGAGCTAATTAAACAGATTGAGATTTGCCAG GAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTT
genomic: TCTCCAAAATAAAAAT-CAAGAGCTAATTAAACAGATTGAGATTTGCCAGgtatttgcaa ... cctctcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTT
EST:
gi|193663723|gb|FK611189.1|FK611189EST: ATCTCCAAAAT-AAAATCAAGAGCTAATTAAACAGATTGAGATTTGCCAG GAAGAAAATAAAATTTT
genomic: ATCTCCAAAATAAAAATCAAGAGCTAATTAAACAGATTGAGATTTGCCAGgtatttgcaa ... cctctcctagGAAGAAAATAAAATTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttaataatgtaatttcttatatttggttttggtatcatcatcacctctcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
ccttaat putative branch site (score: 4)
tcatcacctctcct putative PPT
ataatgtaatttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgcaatttcgtatggtgtttccctctccaagtatgccagccttaataatgtaatttcttatatttggttttggtatcatcatcacctctcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG