Sequence
atgc intronic sequence ATGC exonic sequencegtatgattactgatttacctcattgatttcattttaaaatatatttttttcttggctagaaaacatgacgatttccaatagtttatttgttcaagttggcttttaattttcctccaatgctgcattgctgctttagGTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCTCAATGTTTCTCTGCAGAGATGTATTCAGCAG
Basic information
species | Glycine max |
transcript | GLYMA19G42990.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G05090.2 (Arabidopsis thaliana), 3'ss of exon 13
gtatgattactgatttacctcattgatttcattttaaaatatatttttttcttggctagaaaacatgacgatttccaatagtttatttgttcaagttggcttttaattttcctccaatgct-gcattgctgctttagGTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCTCAATGTTTCTCTGCAGAGATGTATTCAGCAG
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--------------------------------------gtaagtctcttgatcgattttcaaaggttataattt---atttatcgttagtg-aggctagcaggtttgtttactt-attgctcatattactttcttagGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCTGTACATTTGGAGACTCCACAATGCTTCTCTGCTGAAATGTATTCAGCAG
upper sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 13
gtatgattactgatttacctcattgatttcattttaaaatatatttttttcttggctagaaaacatgacgatttccaatagtttatttgttcaagttggcttttaattttcctccaatgctgcattg-ctgctttagGTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCTCAATGTTTCTCTGCAGAGATGTATTCAGCAG
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----------------------------------------gtatggattcctaatttatattaaat----atttgttgtaatttgagtgaaacattttggtgg-atctttcttttgat--tgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTG
upper sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S84_75V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgattactgatttacctcattgatttcattttaaaatatatttttttcttggc-tagaaaacatgacgatttccaatagtttatttgtt-caagttggcttttaattttcctccaatgctgcattgctgctttagGTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCTCAATGTTTCTCTGCAGAGATGTATTCAGCAG
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---------------------------------tggtgaca-attttacacttgacattaatcgtataattgttgattagattcaattttttactatatggaactta--tgatggataagactg-gttgtggcat-agGTGAGTGTGCCAGCATGGTTCACAATGGATACAAGGTTAGGAAGCATGTCTGTGCATCTCGACACGCCTCAGTGTTTCTCAGCAGAAATGTATGCTGTTGMapped 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|27426441|gb|CA937961.1|CA937961EST: GTTTCGTTTGAGGAGAAAAAGGAAGAGCTATTTGAGATG GTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCA
genomic: GTTTCGTTTGAGGAGAAAAAGGAAGAGCTATTTGAGATGgtatgattac ... gctgctttagGTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCA
EST:
gi|207840411|gb|GD812172.1|GD812172EST: GTTTCGTTTGAGGAGAAAAAGGAAGAGCTATTTGAGATG GTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCA
genomic: GTTTCGTTTGAGGAGAAAAAGGAAGAGCTATTTGAGATGgtatgattac ... gctgctttagGTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttgttcaagttggcttttaattttcctccaatgctgcattgctgctttagGTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCTCAATGTTTCTCTGCAGAGATGTATTCAGCAG
ttttaat putative branch site (score: 3)
ctgcttt putative PPT
ttttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattactgatttacctcattgatttcattttaaaatatatttttttcttggctagaaaacatgacgatttccaatagtttatttgttcaagttggcttttaattttcctccaatgctgcattgctgctttagGTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCTCAATGTTTCTCTGCAGAGATGTATTCAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG