Sequence
atgc intronic sequence ATGC exonic sequencegtgaggctcattttttgggctatctcagacctagttttctaacctcatacttctctgtatactttctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
Basic information
species | Glycine max |
transcript | GLYMA20G32030.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 11
gtgaggctcattttttgggctatctcagacctagtttt-ctaacctcatacttctctgtatactttctcttaattcttttcct---cctcttgtttt--ccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
|| | | | ||| | | || |||| | ||| ||| | || | | | | | | | | | ||| | | ||||| || || || || ||||| ||||| || ||||||||||||||||| || || |||||||| || |||||||
-----gcgacagaataagagtgtcttacagctgattttacccacccaatattattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 11
gtgagg-ctcattttttgggctat-ctcagaccta--gttttctaacctcatacttctctgtatactttctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
|| || || || || | ||| ||||| || |||| | | | || |||| ||| | | | | | || || | || | || |||||||||||||| |||||||| || ||||| || ||||| ||||| ||||| || || || || ||||| ||||||||||
gtatggtcttccttattcagttatgttcagagctgttgtttataagtccaacttttgtctggatagtatatttaatttgttcttcttgtttt-ctttccatagCATCCAGGAACAACCATAGTCACGGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTG
upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S152_87V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------------------------------------------gtgaggctcattttttgggctatctcagacctagttttctaacctcatacttctctgtatactttctcttaattcttttcctcctcttgtt---ttccata----gCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
|| | | || | ||||| || |||| | || | | |||||| | ||| | | || || |||| || ||| |||||||||||| ||||||||||||||||||||||| || ||||| ||||| || || ||||| ||||||| |
gtaaaactagcatgagatatctgatatgttaaagcattttacagcggtgaagaaattaacgactttgtctatcacatcaaaagttaacatggctt-tcgtagaacgtatacatgctcagagtggttaaacttaatttgtggtgttttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACGACTTTCATTGAACAGAAACTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatacttctctgtatactttctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
tcttaat putative branch site (score: 3)
tatactttctcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggctcattttttgggctatctcagacctagttttctaacctcatacttctctgtatactttctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA