Sequence
atgc intronic sequence ATGC exonic sequencegtgaggctcatttttttagctatctcagacctagtttaacctcatacttctctgtatacttcctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
Basic information
species | Glycine max |
transcript | GLYMA10G35490.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 11
--------gtgaggctcatttttttagct-atctcag--acctagtttaacctcatacttctctgtatacttcctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
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gcgacagaataagagtg--tcttacagctgattttacccacccaatattattcgatgctactgca-gtgattgccactaacaaatccattgctctgatact----agCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
upper sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 11
gtgagg-ctcatttttttagctat-ctcagaccta--gttta---acctcatacttctctgtatacttcctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
|| || || || || || ||| ||||| || ||||| | | || |||| ||| | | | | || || | || | || |||||||||||||| |||||||| || ||||| || ||||| ||||| ||||| || || || || ||||| ||||||||||
gtatggtcttccttattcagttatgttcagagctgttgtttataagtccaacttttgtctggatagtatatttaatttgttcttcttgtttt-ctttccatagCATCCAGGAACAACCATAGTCACGGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTG
upper sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 10
lower sequence: PP1S152_87V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------------------------------------------gtgaggctcatttttttagctatctcagacctagtttaacctcatacttctc---tgtatacttcctcttaattcttttcctcctcttgtt---ttccata----gCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
|| | | ||| ||||| || | | ||||| | | | |||||| | ||| | | || || |||| || ||| |||||||||||| ||||||||||||||||||||||| || ||||| ||||| || || ||||| ||||||| |
gtaaaactagcatgagatatctgatatgttaaagcattttacagcggtgaagaaattaacgactttgtctatcacat-caaaagttaacatggctttcgtagaacgtatacatgctcagagtggttaaacttaatttgtggtgttttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACGACTTTCATTGAACAGAAACTGGMapped 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|193490892|gb|FK455107.1|FK455107EST: TCAACAGGAATCGTTTAATTGCCTTAATGGCAGCTATTGTTCTTGAGGAA CATCCTGGAACAACTATTG
genomic: TCAACAGGAATCGTTTAATTGCCTTAATGGCAGCTATTGTTCTTGAGGAAgtgaggctca ... ttttccatagCATCCTGGAACAACTATTG
EST:
gi|58023217|gb|CX709958.1|CX709958EST: TAATGGCAGCTA-TGTTC-TGAGGGAA CATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTAC
genomic: TAATGGCAGCTATTGTTCTTGA-GGAAgtgaggctca ... ttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatacttctctgtatacttcctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
tcttaat putative branch site (score: 3)
tatacttcctcttaat CT-rich tract
ttaattctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggctcatttttttagctatctcagacctagtttaacctcatacttctctgtatacttcctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA