Sequence
atgc intronic sequence ATGC exonic sequencegtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
Basic information
species | Glycine max |
transcript | GLYMA16G04580.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 7
gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
|| | ||| | || ||||| | || || || || | | || ||| ||| | ||| ||||||||||||| ||||||||||| || |||||| ||||||| || ||||||||| |||| || |||||| | |||||||||||||||||| | |
------------------------------gtaacttattatctttgttctttatcaggttatcctta-gatgcaccattcttaatttatg---tttgta-----------gGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g57940.2 (Oryza sativa), 3'ss of exon 7
gtaaacccttgtgatagttttttc----aatcctgtcaacct--ttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
||||| | | | || | | ||| | | | || | ||| | ||| ||| || || ||| ||| | || | || |||||||| |||||||| ||||| ||||| ||||| || || |||||||||||||| ||||| |||| ||| || |||||| | | || |||||||||||| | |
gtaaaatttaaagtcacttgtgcctgaaaattatatggagctgcatggaatttctcttttgttttctatttcattggt--gttaacattt-ccagtgcatct--tatcattg--ccagGTTTGTACATGGTGATGTCAAACCAGAGAATTTTTTGCTTGGTCATCCTGGGTCAGTTGATGAGAAGAAGCTTTTCCTGATTGATCTTGGTTTAG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 7
gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
| ||||| ||| | ||| | ||| | | |||| | ||||||| || ||| ||| | ||||| || ||||||||||| ||||| ||||| ||| | ||||| |||||||||||| |||| || ||||| | | | | ||||||||||| | |
--------------------------gtaagcaggccttttgaattttctattagcctc---tggatttcactgttcatgttttatttttggaac-------attttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 7
gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
| || | | | ||| ||| || | || || | | | | |||| | |||| | ||| | || | |||||||||||||| ||||||||||| || || ||| |||||||||| |||||||| |||||||||||||| | || ||||| ||||||||| | |
-----------------gtgagctaaaattagctatcttgaac-ctaacgttc--ttagatgtatgtattactg-ttgatttacactaagatcatctgttt------gccagGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTATAGATCTTGGTTTAG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G082099_T01 (Zea mays), 3'ss of exon 1
gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
| || | | | ||| ||| || | || || | | | | ||| | | |||| | || ||| || | | ||| |||||||||||||| ||||||||||| || || ||| |||||||||| |||||||| |||||||||||||| | || |||| ||||||||| | |
-----------------gtgagctaaaattagctatcttgaac-ctaacgttc--ttagatgtatgtattact-attgatttacacta-tga---tcatctgtttg--ccagGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 5
gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
| || | | | ||| ||| || | || || | | | | ||| | | |||| | || ||| || | | ||| |||||||||||||| ||||||||||| || || ||| |||||||||| |||||||| ||||| |||||||| | || |||| ||||||||| | |
-----------------gtgagctaaaattagctatcttgaac-ctaacgttc--ttagatgtatgtattact-attgatttacacta-tga---tcatctgtttg--ccagGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAATATAAGAAGCTTTACCTTACAGATCTTGGTTTAG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 7
gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
| ||| | | | || | | | | | | || | | | |||||| | |||| ||| | || | | ||| |||||||||||||| ||||||||||| || || ||| |||||||||| |||||||| |||| |||||||| | || ||||| ||||| ||| | |
-----------------gtcagccaaaattagctatgttcatc-tgagcgtcc--ttagatgtatgtatgactg-ttgatttaccctaagg----tcctctgtttgg--cagGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
------gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatg----------gttgtgactga-ctaatttttattaatgaa--actcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
| || |||| | | | || | || | | |||| | ||||| || ||| | | |||| || | | | || || | || ||| || |||||||||||||||||||||||||| |||||||||||||||||||| |||||| |||| || || ||||| |||| ||||| ||||||||||| |
gttagtgcgaatttttgttgtcgccaat--aaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtcatgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 7
----------gtaaacccttgtgatagttttttcaatcctgtcaacc-tttaacatta-ccatttattttggcatggttgtgactg-actaatttttat-taatgaaac-tcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
|| | || | ||| ||| | ||| | ||| | ||| | | ||| || | | | |||| ||| ||| | || ||| | || || || ||||||||| || ||||||||||| || ||||||||||| || |||||||| ||| |||| || || || || | || ||||| |||||||||||||
gttagttactatattttttcgtaacttctttgcaaatagtttcattcatttcgctttaactaattacaatgtattatctttcactgtactgattgtcatgctatgttccatccccatatcaaactagGTTTGTCCACGGAGATGTGAAGCCGGAAAACTTTTTACTCGGTCAACCAGGAACAGCAGATGAGAAAAAACTCTACCTTATCGATCTTGGTCTGG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 7
-------------gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaatta-gGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
||| || ||| | ||| | | | | || | | | | || || | ||| | | || | ||||| | | | | || | |||||||||||||||||||||| || || |||||||| ||||||||||||||| | ||||| || |||||| ||| |||||||||||||||| |||
gtgagtactattaataattccatgtttcactttctcagaatcatcctgtctct--cttgagcactttcctcaaagtggcttcttcattctgttaattattgtcatcttttttcttcctcaaccaagGTTTGTGCATGGAGATGTGAAGCCAGAGAACTTTTTACTTGGTCAACCTGGAACTGCTGATGAGAAGAAGCTATTTCTTATTGATCTTGGTTTGGMapped 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|18692787|gb|BM521635.1|BM521635EST: TGCATTGCAGTAGAGGCAATATCAATTCTTGAGAAGCTCCACTTGAAAGG GTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGG
genomic: TGCATTGCAGTAGAGGCAATATCAATTCTTGAGAAGCTCCACTTGAAAGGgtaaaccctt ... attgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
tattaat putative branch site (score: 2)
tgactaatttttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT