Sequence
atgc intronic sequence ATGC exonic sequencegtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
Basic information
species | Glycine max |
transcript | GLYMA11G15010.1 |
intron # | 8 |
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 8
lower sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 7
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctct-cagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
| ||| || || | ||| | || | || || | || ||||||| || | ||||| ||| || || ||||| || || |||||||| |||||||| | ||||| |||||||||||||||||||| ||||||||||||||||| || | ||
------------------------------------------------------gtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctct-cagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
| ||| || || | ||| | || | || || | || ||||||| || | ||||| ||| || || ||||| || || |||||||| |||||||| | ||||| ||||||||||||||||||
------------------------------------------------------gtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 8
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgc-actgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
|| | ||| | || ||| | | ||| | | || | | || || | || | || || | | |||| | || |||| || ||| | | | |||||| || ||||| || || |||||||| ||||||||| | ||||| ||||| ||||| |||||||| || |||||||||||||| || | ||
--------------gtaatacttcatcttgcacttaa-actgtaatattagctcatagccc------tctttattgtgtgataactctaggcttatgatttgtc-ctca--gcaatatttataatc-tatgtctgt---agAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 4
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcaca-aacagtacacgttttgcactg-ctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
| | ||| | ||| || || | | | ||| || | || | || || | | || || || || |||| | | ||| | |||||| || ||||| || || |||||||| ||||| || | ||||| ||||||||||| |||||||| || |||||||||||||| || | ||
-----------------------------------acttaaacttcaat-attagtagctcatagccctctttgttatgagataactctgggcttatgatttttttcttaacagtat-----ttatcatctatgtctgt-agAAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGTCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 5
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcaca-aacagtacacgttttgcactg-ctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
|| ||| | || ||| | ||| | ||| || || | | | ||| || | || | || || | | || || || || |||| | | ||| | |||||| || ||||| || || |||||||| ||||| || | ||||| ||||||||||| |||||||| || |||||||||||||| || | ||
--------------gtaacacttcatctttcacttaa----acttcaat-attagtagctcatagccctctttgttatgagataactctgggcttatgatttttttcttaacagtat-----ttatcatctatgtctgt-agAAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGTCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcat-atttttctct-cagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
|| ||| | || ||| | ||| | ||| || || ||| | | |||| || || ||||| || | | | | | | || || || | | ||| |||||| || ||||| || || |||||||| ||||| || | ||||| ||||||||||| |||||||| || |||||||||||||| || | ||
--------------gtaacacttcatctttcacttaa----acttcaat-attagtagctca--tagtcctc--tttgttatg-tgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 7
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattt-tcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
|| ||| | || ||| | ||| | ||| || || | | | |||| || || ||||| || | | | | | ||||| |||| | | ||| | |||||| || ||||| || || |||||||| ||||| || | ||||| ||||||||||| |||||||| || |||||||||||||| || | ||
--------------gtaacacttcatctttcacttaa----acttcaat-attagtagctcata----gccctctttgttatg-tgataactctgggcttatgattttttattaacagtatttatcatctatgtctgt-agAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 9
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaat--gtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACC-ACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
|| ||| | || ||| | ||| | ||| || || | | | |||| || || ||||| || | | | ||| | || |||| | | ||| | |||||| || ||||| || || || ||||| ||||| || | | ||||| ||||||||||| |||||||| || |||||||||||||| || | ||
--------------gtaacacttcatctttcacttaa----acttcaat-attagtagctcata----gccctctttgttatg-tgataactctgggcttatgatttttttcttgacagtatttatcatctatgtctgt-agAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 8
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcaca-aacagtacacgttttgcactg-ctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
|| ||| | || ||| | ||| | ||| || || | | | ||| || | || | || || | | || || | || || |||| | | ||| | |||||| || ||||| || || || ||||| ||||| || | ||||| ||||||||||| |||||||| || |||||||||||||| || | ||
--------------gtaacacttcatctttcacttaa----acttcaat-attagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttaacggtat-----ttatcatctatgtctgt-agAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
| ||| || | | || | | || | | | || || || | | | | | | |||| || || | ||| |||||||| ||||| || |||||||||||||| || || ||||| ||||||||||| || ||||| || |||||||||||||| || | |
-----------------------------------------gtaaaattaatc-actcttttaccattttcttgaaaactttgatttaagcttattggc--tgattagttattacttctattgtctggccattgt---agAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
| | | ||||| || |||| | |||| | | ||| |||| || | || || || | | || || || |||| | | || | |||||| |||||||| |||||||||||||| ||||| ||||||||||| || |||||||| |||||||| || ||||||||||| |||||| | ||
-------gtaagttgcattttctcaggctctcgctt-caactttctccctgtaatttgcatcaaca-----tattct-cattgtcctttattc-----------cttaaa-------ttgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaat-gtgatgcttattttcatatttttctctc--agAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
| || | | || || |||| || || || || || | | || | ||| || ||| | | ||| || | |||||| |||||||| |||||||||||||||||||| || || ||||| || ||||||||||||||||| || |||||||||||||||||| | ||
----------------------------------------------gtcagttttctactt---ccctaaactcactgcatcacttttttctt-tatccagtgattcctttaagattctcattggcctgtttgtcatttgtagAAATCCGCATTGCTAGAATCTTCAACACATATGGTCCTCGAATGAACATCGATGATGGGCGTGTTGTGAGCAACTTCATTGCTCAAGCACTCCG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 8
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
| || | | | | || || | || |||| | | | | ||| || || ||| ||| ||| |||||||||||||||| ||||| |||||||||||||| || |||||||||||||||||||| ||||||||||| || ||||| ||||||||| ||||
----------------------------------------------gtaacttttgtgttttttt--ttttaatcctgaacaaacttcaatgaatatgaagt--tttaatatgtatgttgtttctttatattttggacagAAATACGCATTGCTAGAATTTTCAACACATATGGGCCCCGCATGAATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataa-ctcaat-gtgatgcttattttcatatttttc-tctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
|| | ||| || | | ||| | ||| ||| | || |||| | || | | || | ||| |||| | | ||||||| || | || |||| || ||||| ||||| || ||||||||||| || |||||||| || ||||| || || |||||||||||| | |
--------------------------------------aaggatgcgatgaaatgtagctctgagtgtag-----tagcatcactgaattccaagaagcttggatcttggtcataatctctgctttgctattcgtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGMapped 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: GCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG AAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTG
genomic: GCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCGgtaattcctt ... tttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
caataac putative branch site (score: 2)
cttattttcatatttt putative PPT
ttattttcatattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA