Sequence
atgc intronic sequence ATGC exonic sequence...cccccatattttagttcatttaatctcaatgtatccctgttttttttttttttgtgtttctgaatgttgctttgttcctgttcatgaatttgttgtgcagTTATGTGCTAGGAGCAGTTTTCTTGCAGCTTTGTCAAGTGTTAAGGCTTGGAGAGCACCCAATTGTTCAAAAGCCTGTTGATCCAAGTCTTTTTATTCAT
Basic information
species | Glycine max |
transcript | GLYMA16G03970.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G03970.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0056g01250.t01 (Vitis vinifera), 3'ss of exon 8
-cccccatattttagttcatt--taatctcaatgtatccctgttttttttttttttgtgtttctgaatgt-tgctttgttcctgttcatgaatttgttgtgcagTTATGTGCTAGGAGCAGTTTTCTTGCAGCTTTGTCAAGTGTTAAGGCTTGGAGAGCACCCAATTGTTCAAAAGCCTGTTGATCCAAGTCTTTTTATTCAT
| ||||| |||||| ||| | || | | || ||| || ||||| | |||||| || | | | |||| |||||||||||||| || || || || |||||||||||| || || |||| |||| |||||| || || |||||||| |||||||| || || ||||||||||||
gtaaggagattttgtttcattaataaaattctgatagttgtatcttgatttagcttacacttctgcgcttatgctttac----gtccttttaattgtattgcagTTATGTGCTGGGTGCTGTATTTTTGCAGCTTTGTAAACTGCTAAGTCTTGAAGAGCATCCCATCGTTCAAAAACCTGTTGACCCTAGCCTTTTTATTCAT
upper sequence: GLYMA16G03970.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ17728 (Selaginella moellendorffii), 3'ss of exon 5
cccccatattttagttcatttaatctcaatgtatccctgttttttttttttttgtgtttctgaatgttgctttgttcctgttcatgaatttgt---tgtgcagTTATGTGCTAGGAGCAGTTTTCTTGCAGCTTTGTCAAGTGTTAAGGCTTGGAGAGCACCCAATTGTTCAAAAGCCTGTTGATCCAAGTCTTTTTATTCAT
| || | || | | ||| ||| | | ||| || ||| | ||||| ||| |||||||||||||||| | || || ||| | || || | | |||| ||||| |||||||||||||| ||||||||||| ||||| |||
-------------------------------------------gtaagttgtggtcgattttcgtgtgacttccctaacgctca-gaccttgcatctctgcagATATTTGCTAGGAGCAGTTTTTCTCCAACTATGTACCCTATTGAGATTAGATCAGCATCCAATGGTTCAAAAGCCTGTGGATCCAAGTCTGTTTATCCAT
upper sequence: GLYMA16G03970.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ16257 (Selaginella moellendorffii), 3'ss of exon 4
--------------------------------------------------------cccccatattttagttcatttaatctcaatgtatccctgttttttttttttttgtgtt---tctgaatgttgctttgttcctgttcatgaatttgt---tgtgcagTTATGTGCTAGGAGCAGTTTTCTTGCAGCTTTGTCAAGTGTTAAGGCTTGGAGAGCACCCAATTGTTCAAAAGCCTGTTGATCCAAGTCTTTTTATTCAT
|| || | | || |||| || | || | | | | | ||||| | | | ||| ||| || | ||| || ||| | ||||| ||| |||||||||||||||| | || || ||| | | || | | |||| ||||| |||||||||||||| ||||||||||| ||||| |||
gtagagttttcctcgtatacgaactcaagctttggcgcttgtagacagggaaataaaccatatctgctgattgatttc-tcggactgcctacaaaccagtgtgtaagttgtggtcgattttcgtgtgacttccttaacgctca-gaccttgcatctctgcagATATTTGCTAGGAGCAGTTTTTCTCCAACTATGTACCCTACTGAGATTAGATCAGCATCCAATGGTTCAAAAGCCTGTGGATCCAAGTCTGTTTATCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttgtgtttctgaatgttgctttgttcctgttcatgaatttgttgtgcagTTATGTGCTAGGAGCAGTTTTCTTGCAGCTTTGTCAAGTGTTAAGGCTTGGAGAGCACCCAATTGTTCAAAAGCCTGTTGATCCAAGTCTTTTTATTCAT
atgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccccatattttagttcatttaatctcaatgtatccctgttttttttttttttgtgtttctgaatgttgctttgttcctgttcatgaatttgttgtgcagTTATGTGCTAGGAGCAGTTTTCTTGCAGCTTTGTCAAGTGTTAAGGCTTGGAGAGCACCCAATTGTTCAAAAGCCTGTTGATCCAAGTCTTTTTATTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
cccccat
- - - - - - - - - - - - - caatgta
- - - - - - - - - - - - - - - - -tccctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaat