Sequence
atgc intronic sequence ATGC exonic sequencegtttaccacatccccccttcctccaggttgtagatgttctcattttgagtgtgaaagttatctgagttatttctggttctatgttcaacagGAAAAGAATCCAAACATCAAGTGCTTCCTCTTAGATCCTCCTGGCTCTGGTTTGTTTAATAAGGTAACCAGGGGAGTGATGTACACCAAAGAGGAGGCGG
Basic information
species | Glycine max |
transcript | GLYMA14G01780.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G01780.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g11660.1 (Oryza sativa), 3'ss of exon 4
gtttac-cacatccccccttcctccaggttgtagatgttctcattttgagtgtgaaagttatctgagttatttctggttctatgttcaacagGAAAAGAATCCAAACATCAAGTGCTTCCTCTTAGATCCTCCTGGCTCTGGTTTGTTTAATAAGGTAACCAGGGGAGTGATGTACACCAAAGAGGAGGCGG
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gtttgcatgcttcttatgttatttc---ttctgtatatttctttctcacatgtagaccttttttatgcctatgctataatcaaat---atagGAAAAGAACACAAACATCAAATGCTTCTTAATGGACCCACCTGGATCTGGTCTGTTCAATAAGGTTACTAGAGGGGTGATGTACACAAAAGAGGAAGCTG
upper sequence: GLYMA14G01780.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G128744_T01 (Zea mays), 3'ss of exon 2
gtttaccacatccccccttcctccaggttgtagatgttctcattttgagtgtgaaagttatctgagttatttctggttctatgttcaacagGAAAAGAATCCAAACATCAAGTGCTTCCTCTTAGATCCTCCTGGCTCTGGTTTGTTTAATAAGGTAACCAGGGGAGTGATGTACACCAAAGAGGAGGCGG
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----gttagatgcttactatttttttgtt-tgtatatttt-atcctagataaacatcttttatga-----ctatggtactcc-ttatgtagGAAAAGAACAGGAGCATCAAATGTTTTTTAATGGACCCTCCTGGATCTGGTCTGTTCAATAAGGTTACCAGAGGGGTGATGTACACAAAAGAGGAGGCCG
upper sequence: GLYMA14G01780.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G55880.1 (Arabidopsis thaliana), 3'ss of exon 4
-----gtttaccacatccccccttcctccaggttgtagatgttctcattt--tgagtgtgaaagttatctgagttatttctggttc-----tatgttca-acagGAAAAGAATCCAAACATCAAGTGCTTCCTCTTAGATCCTCCTGGCTCTGGTTTGTTTAATAAGGTAACCAGGGGAGTGATGTACACCAAAGAGGAGGCGG
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gtataattactcagggcttatactaatcaaagatgtaagaatgagtaattcgtggatgttataagcaaaagaaaaactcataacttgttggtgcatttatacagGATAAGAATGAAAGAGTTAAATGTTTTCTGATTGATCCTCCTGGATCTGGTCTGTACAATAAAGTAACACGGGGAGTGATGTACACAAGAGAAGAAGCTG
upper sequence: GLYMA14G01780.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g00380.t01 (Vitis vinifera), 3'ss of exon 5
---gtttaccacatccccccttcctccaggttgtagatgttctcattttgagtgtgaaagttatctgagttatttctggttctatgttcaacagGAAAAGAATCCAAACATCAAGTGCTTCCTCTTAGATCCTCCTGGCTCTGGTTTGTTTAATAAGGTAACCAGGGGAGTGATGTACACCAAAGAGGAGGCGG
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gtcacttttcctctccatctttttatcaaaccttt--tttctgcacttcaattgtgcaaggaaagtcactg--tagtcattacatgttcaacagGAAAAAAGTCCAAATATCAAATGCTTTCTGATTGACCCTCCTGGTTCTGGCTTGTTCAATAAGATAACAAGGGGAGTAATGTACACTAGAGAGGAGGCTGMapped 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|9820085|gb|BE555595.1|BE555595EST: CAGCAGCGGGTACCGGTGGTACTGTGGCTGGTGTTTCTAAGTTTCTTCAG GAAAAGAATCCAAACATCAAGTGCTTCCTCTTAGATCCTCCTGGCTCTGGT
genomic: CAGCAGCGGGTACCGGTGGTACTGTGGCTGGTGTTTCTAAGTTTCTTCAGgtttaccaca ... tgttcaacagGAAAAGAATCCAAACATCAAGTGCTTCCTCTTAGATCCTCCTGGCTCTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcattttgagtgtgaaagttatctgagttatttctggttctatgttcaacagGAAAAGAATCCAAACATCAAGTGCTTCCTCTTAGATCCTCCTGGCTCTGGTTTGTTTAATAAGGTAACCAGGGGAGTGATGTACACCAAAGAGGAGGCGG
aaagttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaccacatccccccttcctccaggttgtagatgttctcattttgagtgtgaaagttatctgagttatttctggttctatgttcaacagGAAAAGAATCCAAACATCAAGTGCTTCCTCTTAGATCCTCCTGGCTCTGGTTTGTTTAATAAGGTAACCAGGGGAGTGATGTACACCAAAGAGGAGGCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG