Sequence
atgc intronic sequence ATGC exonic sequence...attttaaaatatctagttgaagagttttctttcctttccttacctcaccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
Basic information
species | Glycine max |
transcript | GLYMA04G01720.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G01720.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g49560.1 (Oryza sativa), 3'ss of exon 4
attttaaaatatctagttgaagagttttctttcctttccttacctcaccagagtattgaaaaccatgat--gtatttacatctttttaattatattttg---cagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
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-atttaacatatttgtttacagcagtttttattcactgtatatgctaata----atccaaagttttggttcatactcagtaccctttccttgtacattgatatagGTGCGGAAAAATAGTAAACATTGTCGGAGTTGTGACAAATGTGTTGATGGTTTTGATCATCATTGCCGG
upper sequence: GLYMA04G01720.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G010011_T02 (Zea mays), 3'ss of exon 5
attttaaaatatctagttgaagagttt-tctttcctttccttacctcaccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
||| | || | | | ||| | ||| | | ||| || | || || | || | | | || ||| | | | | ||||||| || ||| ||||| ||||||||||| ||||| ||||||||||| |||||||| || || |||
tctttgtattaattttcagtgcactttatgtttggacacatggtatcaacacaaagttttaatcgatactaagtgcagttccctttgtat-tgtgatacagGTGCGCAAACATAGCAAGCACTGTCGAAGTTGCGACAAGTGTGTTGATGGGTTTGATCATCACTGCCGG
upper sequence: GLYMA04G01720.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G33640.1 (Arabidopsis thaliana), 3'ss of exon 4
attttaaaatatctagttgaagagttttctttcctttccttacctcaccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
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---------------gtatagtacatttttaccttctggttaga--agcttctcattgcatcttgtactgtaacagcacattcttt------tcttgaagGTACGTATGTTTAGCAAGCACTGTCGAAGTTGTGGCAAGTGTGTAGATGGGTTTGATCACCATTGCCGG
upper sequence: GLYMA04G01720.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0122g00920.t01 (Vitis vinifera), 3'ss of exon 4
-attttaaaata--tctagttgaagagttttctttcctttccttacctcaccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
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aatttcagtgtggtctttgttaaaaccttgaattcagtggtcagattttggcttaaaataaagaag-atcattcaagaatgttgattttgttcc--tctgtagGTACGCAAATTCAGCAAACATTGCAGAAGTTGTGACAAATGTGTCGATGGGTTTGATCATCATTGTCGT
upper sequence: GLYMA04G01720.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
---attttaaaatatctagttgaagagttttctttcctttccttacctcaccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
| || || ||| | | | ||| | | | || ||| | |||| |||| | | | ||| | |||| |||| | ||||| ||||| ||||| |||| || ||||||||||||||||| ||||| ||||||||||||
gttgtattggtcaatgcttgtgaggggatctctctagcagcaaaatttctttt--gtact-aaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
upper sequence: GLYMA04G01720.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36891 (Selaginella moellendorffii), 3'ss of exon 3
attttaaaatatctagttgaagagttttctttcctttccttacctcaccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
||| | | | | |||||| | || |||| | | | ||| |||| | |||||| || ||||| || || ||||||||||| ||||| || |||||||||||||| ||||||||||||||
---------------------------------gtttgagttctttccgtgagtat-gtcgacattgatttgataag----tttggtttatctcacgcagGTTCATAAGTTCAGCAAACATTGTCGAAGCTGTGATAAGTGTGTTGATGGATTCGATCACCATTGTCGT
upper sequence: GLYMA04G01720.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ33542 (Selaginella moellendorffii), 3'ss of exon 3
attttaaaatatctagttgaagagttttctttcctttccttacctcaccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
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---------------------------------gtttgagttctttccgtgagtat-gtcgacattgatttgataag----tttggtttatctcacgcagGTTCATAAGTTCAGCAAGCATTGTCGAAGCTGTGATAAGTGTGTTGATGGATTCGATCACCATTGTCGTMapped 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|151395855|gb|EV265732.1|EV265732EST: AACAGTCTGGGGAAGAGGAGGCTTTGTTCTGCACTTTGTGCAATGCTGAG GTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGA
genomic: AACAGTCTGGGGAAGAGGAGGCTTTGTTCTGCACTTTGTGCAATGCTGAGgttgatacga ... tattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
ttttaat putative branch site (score: 3)
atgatgtatttacatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttaaaatatctagttgaagagttttctttcctttccttacctcaccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - cctttcc
- - - - - - - - - - - - - - - - - - - - - cctcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgat