Sequence
atgc intronic sequence ATGC exonic sequence...taggaatttggaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
Basic information
species | Glycine max |
transcript | GLYMA11G15010.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 7
taggaatttggaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
| | | | | || | | | | || || || || | |||| | ||| | | | || | || | | | ||||||| ||||||| ||||| ||||| |||||||| |||||||| |||||||||| ||||| ||||||||||| || |
--gtacgtctgttctatca-caaatacactacat-ttatcctatattttcttaatctagtgcaaagttca---cttacttgaattgatttacttcatcagGAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 8
-taggaat-ttggaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
|| | || ||| || || || || | | | || || | || | || | | ||| | | | | | |||| ||| ||||||||||||||||||| |||||||| ||||| | ||||||||||| ||||| ||||||||||| || |
gtaaatttcttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagtttttatttaactttttttct-atcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 7
taggaatttg---gaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
|||||| ||| || || || || | | | || || | || | || | | ||| | | | | | |||| ||| ||||||||||||||||||| |||||||| ||||| | ||||||||||| ||||| ||||||||||| || |
-gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagtttttatttaactttttttct-atcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
taggaatttg---gaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
|||||| ||| || || || || | | | || || | || | | | | ||| | | | | | |||| ||| ||||||||||||||||||| |||||||| ||||| || ||||||| || ||||| ||||||||||| || |
-gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttct-atcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
taggaatttg---gaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
|||||| ||| | || || || | | | || || | || | || | | | || | | | | |||| ||| ||||||||||||||||||| |||||||| || || || ||||||||||| ||||| | ||||||||| || |
-gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttat--ttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 7
taggaatttggaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataa--aaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
| || || | | | | | ||||||| | | ||| || | | | | | | || | | || | | | ||||||| |||| |||||||||||||| |||||||| ||||| || ||||||| || ||||| ||||||||||| || |
--gtaaatttgttcatctgacaattgcaatatatttgctttgatt--ttcataaattatcattcaagttatcttacggttttgatttgattttttctatcagGAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 4
taggaatttg---gaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTC-GGAGTTGTTATGATGAGGGCAAGCGTGTTGCA-GAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
|||||| ||| ||| || | || | | | || || | || | || | | ||| | | | | ||| ||| ||||||||||||||||||| |||||||| ||| || || |||||||| || ||||| ||||||||||| || |
-gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttacagtttttatttaac--ttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 5
-taggaatttggaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
|| | || | |||| || | ||||| || || | || | | || | | | || ||| || | || | ||| ||| | || ||||||||||| || || |||||||| || ||| | ||||||||||| |||||||| ||||| || |
gtaagtcattata-tgactattatttgtaata-atctcagtttatcaatttatgaactaacacaaaatgaatttgctggtggca--------cattataagGTGTTAGAAGCTGTTATGATGAAGGAAAACGTGTTGCCGAGACTCTTATGTTTGATTACCATAGGCAACATGGGATTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
-taggaatttggaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
||||| | | | | || | |||||| | | |||| | || ||| | | || | | || | | ||| ||||| ||| ||| |||| ||||||||||| |||||||||||||| || || ||||||||||| || || ||||| |||||||| |
gtaggagtaaacacttatca--gcttttaattctcaacttatctgcgtgtc----aat-tcacattctta-taacttggtttc-----tat-tatga-tagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 6
taggaatttggaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
|| | |||| | || ||| | | | | | | || || | ||||| | || || ||| | ||| || ||| ||||||||||| ||||| || |||||||| || || ||||| ||||||||||| || || || || ||||| || |
-gtaaacctcaaatgttc-tcatcttatagaggaatcttcttgc-atttcagtttttacagctttgtaaa----cttaacctggttgctattatcaaaagGGGTTCGGAGTTGCTATGACGAAGGCAAGCGGGTAGCCGAAACCTTGATGTTTGACTACCACAGACAACATGGCATTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
taggaatttggaatgaccatcgactttaatat--ataccatatcattatctcttggaatgttgctttatcaatagc-ctaaacataaaaatatgt-atgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
| | | | | || ||||| || | ||| || | | || ||| |||| || | || || ||| | | | ||||| || ||||| || ||||||||||| |||||||| || || |||||||||||||||||||||||||| ||||| || |
-aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaatt---atgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------taggaatttggaatgaccatcgactttaatata--taccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtat-gaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
|| |||| |||||| | | | | | | | || || | | | || ||| ||| | ||| | | |||||| | || || ||||| ||||| ||||||||||| || ||| | |||||||| || |||||||||||||| | |
gtaaatccaactcacgttacacgcttggtgc-accatcacgctctgtgcagtttctgaactctgatacacaatcattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGMapped 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|22525432|gb|BU084243.1|BU084243EST: TCTTGTGCATCCACAACCAGAAAGCTATTGGGGCAATGTAAACCCCATTG GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
genomic: TCTTGTGCATCCACAACCAGAAAGCTATTGGGGCAATGTAAACCCCATTGgtacttacac ... gtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
EST:
gi|18040716|gb|BM309010.1|BM309010EST: CTTGTGCATCCACAACCAGAAAGCTATTGNGGGCA-TGTAAACCCCATTG GAGTTCGGAATTGTTATGATGAGGGCAAGCGTGTTGCAAAAACTTTGATGT
genomic: CTTGTGCATCCACAACCAGAAAGCTATTG-GGGCAATGTAAACCCCATTGgtacttacac ... gtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
gcctaaa putative branch site (score: 3)
taaacataaaaatatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taggaatttggaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - -ggaatga
- - - - - - - - - - - - - - - - - - catatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata