Sequence
atgc intronic sequence ATGC exonic sequence...agtagtactgatatgaatgagatgtgctttttgttgcagaacatgtatgctcaattgttgcctcttgctttgcctgcaccaccaatgcctggaatgggagGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTCCTTATGGTATGCCACCCATGGGCAGCAGTTTTTGAAGAGTATAGCATGA
Basic information
species | Glycine max |
transcript | GLYMA14G06340.2 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 27
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 29
-------------------------------------------------agtag-tactgatatgaatgagat-gtgctttttgttgcagaacatgtatgctcaattgttgcctcttgctttgcctgcaccaccaatgcctggaatgggagGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTCCTTATGGTATGCCACCCATGGGCAGCAGTTTTTGAAGAGTATAGCATGA
||||| | | || || || | | || |||||||||||||||| |||||| | |||||||| |||||||| || || ||| ||||| || |||||| || |||||||| | ||| ||||| || |||
gtaatctatagagattgctcttcttttggttattattctgttattatttagtaggcagcatgacgagtggtattacattgtatggtgcagAACATGTATGCCCAATTGCTTCCTCTTGCCTTGCCTGCTCCTCC------TGGTATGGGCGG------TCCTCCACCGCCAATGGGGATGCCGGGCATGCCTCCGATGGGCG-------------------------------------------------
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 27
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 29
-------------------------------------------------agtag-tactgatatgaatgagatg----tgctttttgttgcagaacatgtatgctcaattgttgcctcttgctttgcctgcaccaccaatgcctggaatgggagGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTCCTTATGGTATGCCACCCATGGGCAGCAGTTTTTGAAGAGTATAGCATGA
||||| | | || | || || | | || |||||||||||||||| |||||| | ||||| || |||||||| ||||| ||| ||||| || |||||| || |||||||| | ||| ||||| || |||
gtaatctatagagattgctcttcttttggttattattctgttattatttagtaggcagcatgacgagcggtattacattgttgtatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACC------TGGTATGGGCGG------TCCTCCACCGCCAATGGGGATGCCGGGCATGCCTCCGATGGGCG-------------------------------------------------
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 27
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------------agtagtactgatatgaatgagatgtgctttttgttgcagaacatgtatgctcaattgttgcctcttgctttgcctgcaccaccaatgcctggaatgggagGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTCCTTATGGTATGCCACCCATGGGCAGCAGTTTTTGAAGAGTATAGCATGA
| ||| || |||| || | | | | ||||||||||||||||| |||||| | ||||||||||||||||| || ||||||||||| ||||| ||| ||||| ||||| |||||||| |||| ||||| ||||
gtacatctaaatcttcattcacatgttctgttcgtgtaattaatcatttcatcctgaggcagt--tggcatga-caagttacgttccattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCTGGCATGGGTGGC------CCTCCACCTCCGATGGGTGGGATGGGCATGCCTCCAA-------------------------------------------------------
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 27
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------------agtagtactgatatgaatgagatgtgctttttgttgcagaacatgtatgctcaattgttgcctcttgctttgcctgcaccaccaatgcctggaatgggagGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTCCTTATGGTATGCCACCCATGGGCAGCAGTTTTTGAAGAGTATAGCATGA
| ||| || |||| || | | | | ||||||||||||||||| ||| || | |||||||| ||||||| || |||||||| || ||||| ||| ||||| ||||| ||||| ||| |||| ||||| || |
gtacatctaaatcttcactcacatgttctgtttgtgtaattaaccatttcatgctgaggcagt--tggcatga-caagctacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGC------CCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA-------------------------------------------------------
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 27
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 29
----------------------------------------------------agtagtactgatatgaatgagatgtgctt--tttgtt-----gcagaacatgtatgctcaattgttgcctcttgctttgcctgcaccaccaatgcctggaatgggagGC---------TTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTCCTTATGGTATGCCACCCATGGGCAGCAGTTTTTGAAGAGTATAGCATGA
|| ||| | | || | | |||| || |||||| |||||||||||||| ||| ||||||| |||||||| ||||||||||| ||||| ||||||||||| | || |||||| || | |||||| ||
gtactacttatgacacagctacactggatatcatccgactctttatcttgacagatacacttaaaggagtaatatgtttttcttttgtttttaaacagAACATGTATGCCCAAATGTTGCCACTTGCTTTACCTGCACCACCGATGCCAGGAATGGGAGGTGGTGGTGGGTATGGTCCTCCACCACAAATGGGCGGTA----------------------------------------------------------------------
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 27
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 29
-------------------------------------------------------------agtagtactgatatgaa-tgagatgtgctttttgttgcagaacatgtatgctcaattgttgcctcttgctttgcctgcaccaccaatgcctggaatgggagGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTCCTTATGGTATGCCACCCATGGGCAGCAGTTTTTGAAGAGTATAGCATGA
| | | || ||| || | | |||| || | ||||||| ||||||||||| ||| |||| ||||||||||||||||| || ||||| || |||||||| || || || | | || || |||
agtggcatggcgtttttcttcatccccttctgttattattgaccatcttaatttatagctgggcaat-ctaatagaaactaatatgttacattggctgcagAATATGTATGCTCAGTTGCTGCCCCTTGCTTTGCCTGCACCTCCGATGCCCGGCATGGGAGGAGCTGGGAT---------GGCAGGAGGTTTTGTTCCACCTCCCATGG----------------------------------------------------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|33387287|gb|CA850494.1|CA850494EST: AGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAG GCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTC
genomic: AGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGgcaggtaggt ... ggaatgggagGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgctcaattgttgcctcttgctttgcctgcaccaccaatgcctggaatgggagGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTCCTTATGGTATGCCACCCATGGGCAGCAGTTTTTGAAGAGTATAGCATGA
aattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtagtactgatatgaatgagatgtgctttttgttgcagaacatgtatgctcaattgttgcctcttgctttgcctgcaccaccaatgcctggaatgggagGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTCCTTATGGTATGCCACCCATGGGCAGCAGTTTTTGAAGAGTATAGCATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - gaatgag
- - - - - - - - - - - - tgctttt
- - - - - - - - - - - - - - - -tgttgca
- - - - - - - - - - - - - - - - - - - - - - gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgcc