Sequence
atgc intronic sequence ATGC exonic sequence...tattttgtttatttttttgtgcttgtgtataatatcttttggtaatgatgtttcatttgaagccaaataaagatgttttcatatattgacgccttttcagCTCTGCTGACATATGGAGTGTGGGTTGTACTGTGATTGAGATGGCCACTGGAAAGCCTCCCTGGAGTCAGCAATACCAACAAGAG
Basic information
species | Glycine max |
transcript | GLYMA19G42340.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g21510.1 (Oryza sativa), 3'ss of exon 7
tattttgtttatt-tttttgtgcttgtgtataatatcttt-tggtaatgatgtttcatttgaagccaaataaagatgttttcatatattgacgccttttcagCTCTGCTGACATATGGAGTGTGGGTTGTACTGTGATTGAGATGGCCACTGGAAAGCCTCCCTGGAGTCAGCAATACCAACAAGAG
| | ||| || || | ||| || || | | | | | || ||||| | | | | || | | | | |||||||||| ||||| ||||||||||| || || || ||||| ||||| ||||| || || || ||||| ||||| ||||| |
-aagtaaaacattattgttattcttaaaagctatttcagtatcatgttatttttctatttgttcttactttttagctgatccgtactatc-catcctctcagCTCTGCAGACATCTGGAGTGTGGGATGCACAGTTATTGAAATGGCTACTGGTAAACCACCATGGAGCCAGCAGTACCAGGAG---
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G09000.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------tattttgt---ttatttttttgtgcttgtgtataatatcttttggtaatgatgtttcatttgaagccaaataaagatgttttcatatattgacgcct-----tttcagCTCTGCTGACATATGGAGTGTGGGTTGTACTGTGATTGAGATGGCCACTGGAAAGCCTCCCTGGAGTCAGCAATACCAACAAGAG
| |||||| | || | | ||||| || || || | || || || | || | ||| || || ||| | | | || | |||||||||||||||||||||| || || ||||| || ||||| |||| ||||| ||| |||| ||||||||||| || || |
gtaagaaaccaagcgtgctcgtaaatgcaaaattagatgttttgtaactgatactcatacaattgtggctattaa-ttgtagtcctggtgacttatgtc---ccatatttttgatttctcacaaacctgtggctattgttctcagCTCTGCTGACATATGGAGCGTCGGCTGTACAGTTATTGAAATGGTGACTGGGAAGGCTCCTTGGAGTCAGCAGTATAAAGAG---
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 7
tattttgtttatttttttgtgcttgtgtataatatctt-ttggtaatgatgtttc--atttgaagccaaataaagatgttttcatatattgacgccttttcagCTCTGCTGACATATGGAGTGTGGGTTGTACTGTGATTGAGATGGCCACTGGAAAGCCTCCCTGGAGTCAGCAATACCAACAAGAG
| | | |||| || || |||| || | | ||| |||||| | | | || || | || | || || | | | || | ||||| ||||| ||||||||||| || ||||| || |||||||||||||||||||||||||| ||||| || | |||||| |
-aatctcattatgcttctgcatctgtg-atgttctgacattgataatgaagatcacaaattcttgctatattattctgattattttcaa-aataatttattagCTCGGCTGATATATGGAGTGTTGGATGTACCGTTATTGAGATGGCCACTGGAAAGCCTCCTTGGAGCCAAAAGTACCAAGAG---
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ32294 (Selaginella moellendorffii), 3'ss of exon 5
tattttgtttatttttttgtgcttgtgtataatatcttttggtaatgatgtttcatttgaagccaaataaagatgttttcatatattgacgccttttcagCTCTGCTGACATATGGAGTGTGGGTTGTACTGTGATTGAGATGGCCACTGGAAAGCCTCCCTGGAGTCAGCAATACCAACAAGAG
| | || | |||| | | | | ||| ||||| ||| | || ||| |||| || |||||||||||||||||||| ||||| ||||||||||| || || ||||| || |||||| | || | ||| |
------------------------------------gtaggcctctgctttttctcgtcttggcttttcaagtgtttttcgtatgt-atcgtcttatcagGCAAGCAGACATATGGAGTGTGGGTTGCACTGTCATTGAGATGGCAACAGGCAAGCCGCCGTGGAGTGATCAGTTTCAAGAG---
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ20963 (Selaginella moellendorffii), 3'ss of exon 5
tattttgtttatttttttgtgcttgtgtataatatcttttggtaatgatgtttcatttgaagccaaataaagatgttttcatatattgacgccttttcagCTCTGCTGACATATGGAGTGTGGGTTGTACTGTGATTGAGATGGCCACTGGAAAGCCTCCCTGGAGTCAGCAATACCAACAAGAG
| | || | |||| | | | | ||| | ||||| ||| | || ||| |||| || |||||||||||||||||||| ||||| ||||||||||| || || ||||| || |||||| | || | ||| |
------------------------------------gtaggcctctgctttttctcgtctgggcttttcaagtttttttcgtatgt-atcgtcttatcagGCAAGCAGACATATGGAGTGTGGGTTGCACTGTCATTGAGATGGCAACAGGCAAGCCGCCGTGGAGTGATCAGTTTCAAGAG---Mapped 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|208162310|gb|GD962201.1|GD962201EST: GATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTT CTCTGCTGACATATGGAGTGTGGGTTGTACTGTGATTGAGATGGCCACTGG
genomic: GATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTTgtaaggacat ... gccttttcagCTCTGCTGACATATGGAGTGTGGGTTGTACTGTGATTGAGATGGCCACTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgtttcatttgaagccaaataaagatgttttcatatattgacgccttttcagCTCTGCTGACATATGGAGTGTGGGTTGTACTGTGATTGAGATGGCCACTGGAAAGCCTCCCTGGAGTCAGCAATACCAACAAGAG
tattgac putative branch site (score: 2)
cgccttttc CT-rich tract
aaataaagatgttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattttgtttatttttttgtgcttgtgtataatatcttttggtaatgatgtttcatttgaagccaaataaagatgttttcatatattgacgccttttcagCTCTGCTGACATATGGAGTGTGGGTTGTACTGTGATTGAGATGGCCACTGGAAAGCCTCCCTGGAGTCAGCAATACCAACAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - -cttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa