Sequence
atgc intronic sequence ATGC exonic sequence...atccattaaatgtataactatgatcttagatgattgtgtgagcttcttgatcagtgttacctttttgttatgctggatttttgtttccaatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
Basic information
species | Glycine max |
transcript | GLYMA14G10960.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G10960.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g39260.1 (Oryza sativa), 3'ss of exon 6
atccattaaatgtataactatgatcttagatgattgtgtgagcttcttgatcagtgttacctttttgttatgctggatttttgtttccaatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
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---------gtaattcttgagaacttttggt-atcatgtttg--tccagactaagatggaatgtcttatattt---atccttatacacatatggttacagGTCTTGAAGAGTGATGATGTGGATTTGATGATCATTGCCAGGGGAACACCTGGATTCTCAGGTGCAGACCTTGCTAACTTGGTTAATGTGGCTGCTCTTA
upper sequence: GLYMA14G10960.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g39250.1 (Oryza sativa), 3'ss of exon 6
atccattaaatgtataactatgatcttagatgattgtgtgagcttcttgatcagtgttacctttttgttatgctggatttttgtttccaatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
| | || | | || | | | || |||| ||| | | | ||| | ||||| || | | || | ||||||| ||||| ||||||||| ||| | |||||||||||| | | ||||||||| ||||| ||||| |||||||| |||||| | || | |||||| | |
--gtaattcttgagaacttttggtatca--tgtttgtccaggct----aaaatggaatgtcttatagttatcct-------tatacacatatgattacagGTCTTGAAGAGTGATGATGTGGATTTGATGATCATTGCCAGGGGAACACCTGGATTCTCAGGTGCAGACCTTGCTAACTTGGTAAATGTGGCTGCTCTTA
upper sequence: GLYMA14G10960.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 6
atccattaaatgtataactatgatcttagatgattgt-gtgagcttcttgatcag-tgttacctttttgttatgctggatttttgtttccaatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
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-------------------gtgattcttgagaactcttgttcctgtgttattcaaatgaaatcgttttctcttaccg---tcctattt---gtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
upper sequence: GLYMA14G10960.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G463032_T01 (Zea mays), 3'ss of exon 5
atccattaaatgtataactatgatcttagatgattgtgtgagcttcttgatcagtgttacctttttgttatgctggatttttgtttccaatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
||||||| || | | | || || | || | | || | | | | | | | ||| | |||| | ||||||||| || ||||||||||||| ||| |||||| || ||||||||||| |||||||| |||||| | || |||||||| | |
-------------------gtgatcttgagaccttttattattttactgtcc-----cactcgtatattgcctcttaccgtcctactcgtttat-tgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCTAGAGGAACACCGGGATTCTCTGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCTCTTA
upper sequence: GLYMA14G10960.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------------------------------------atccattaaatgtataactatgatcttagatgattgtgtgagcttcttgatcagtgttacctttttgttatgc----tggatttttgtttccaatcaaa----tacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
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gtattgtcaccctctaccaaaaattttaaggtgttttttgtacaatgaacactaagttggagtaaaaaagggctctacttttccagtcttgggaaggctttg--cttgtgtgtctatttgca-tggctgaccagtatcaaggttttgcttttccccttggcctaatgtatctaaatactattctacagGTTCTGAAGGGGGATGATGTTGATCTGATGATAATTGCTAGAGGAACTCCTGGGTTTTCAGGTGCTGATCTTGCAAACTTGGTCAATATTGCTGCTCTCAMapped 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|8285572|gb|BE023131.1|BE023131EST: ATCCTGATGTAAAAGGAAGACAGCAGATTTTGGAATCACACATGTCAAAG GTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCT
genomic: ATCCTGATGTAAAAGGAAGACAGCAGATTTTGGAATCACACATGTCAAAGgtattatttt ... tcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgatcagtgttacctttttgttatgctggatttttgtttccaatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
tcttgat putative branch site (score: 4)
tttttgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atccattaaatgtataactatgatcttagatgattgtgtgagcttcttgatcagtgttacctttttgttatgctggatttttgtttccaatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGTAACACCTGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- ccattaa
- - - - - - - - - - - - - - - - - tgtgtga
- - - - - - - - - - - - - - - - - - - - -gcttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgttacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgga