Sequence
atgc intronic sequence ATGC exonic sequencegtgttctataatatctttttccccctctaaactgttgtgacttgtgtccactttcttgttataaatacaaatatactgtattcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
Basic information
species | Glycine max |
transcript | GLYMA05G03970.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 11
gtgttc-tataatatctttttccccctctaaactgttgtgacttgtgtccactttcttgttataaatacaaatatactgt-attcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
||| | | | | | || || |||| || | | || || | | | | || | | | |||| || |||||| ||||| ||||| || |||||| | ||||||||||||||||| ||||||||||| ||||| |||
gtgagcatgtcaaaatcttcatttgtagtagcttgttt--accaattttcagttctgttgtgctcttgaatgctgaccatgaaacaacagGTCCCAAGCAAGTCTGGTTCAGGCACTGAGAACAAGGAGGTTTTGTTGGAGGATCATGATCCAATATGGCTTGAGCTTCGGCAT---------------
upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 10
------------gtgttctataatat--ctttttccccctctaaactgttgtgacttgtgtccactttcttgtt-----ataaatac--aaatatactgtattctta------agGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
| || | | | | | | || | ||| | | || ||| | || || || | | |||| || | || | ||||||| || |||| |||| || |||| ||| |||||| | ||||||||||||||||| |||||||||| || || ||||||||||| || ||
gtgagtacatcagcagcatacagtcttacactgtacctcactagtttaccttattcagttcttactatgtttttgatgcatgactcttaaaatttatgccaccctcaaacaatagGTTCCAAGTAAGAATGGTTCAGCAAATGAGAAAAAGGAGGTTTTGTTGGAGGATCATGATCCAGTATGGCTTGAGCTGCGGCATGCACATATAGCTCAT
upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 10
-------gtgttctataatatcttttt---ccccctctaaactgttgtgacttgtgtccact-ttcttgttataaatacaaatatactg-tattcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
| | || ||| || ||| | || | | || || || | ||| || | | | | | |||||||| | || | ||| || |||| ||| ||||| || |||||||||||||| ||| | |||||||| ||| | ||||||||||| ||||||
ctaaactttaggccatgggatccaaacagggccttaataatgtattcttttccattgcctctgtttatactatggattcttttctctgactgaaatgaagGTTCCAACTAAAAATGGGTCGGCAACTGAAAAAAAGGAGGTCCTGTTGGAGGATCATGACCCTGTCTGGCTTGAGCTTAGGCATGCACATATAGCAGAT
upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgttctataatatctttttccccctctaaactgttgtgactt-gtgtccactttcttgttataaatacaa----atatac-tgtattcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
|| | | || || | | | | |||||| || ||| || |||| | | | | | || | | | || | || || |||| ||||| | || || | ||| ||| ||||| || || || ||||| ||||||||||| ||||| || ||||| ||||||||||| ||||||
-----gtaagttcaagtcttttccgtattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttagATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAGGAACATGATCCTATTTGGCTAGAGCTTCGACATGCACATATAGCAGAT
upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 10
----gtgttctataatatctttttccccctctaaactgttgtgacttgtgtccactttcttgttataaatacaaatatactgtat-tcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
| || | || | | ||| | | | | | ||| | ||| | | | | | | | | | | | || ||||||| || || || ||||||||||| ||| |||||| || ||||||||||||||||||||| | |||||||| || || ||||||||||| ||||||
gtaagccttttccaaattttatttatgcttttggatt----tgatat-tgtttttcctttagctgtgtgtgttgaggaattattcctttttagGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgtgacttgtgtccactttcttgttataaatacaaatatactgtattcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
tattctt CT-rich tract
ttataaatacaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttctataatatctttttccccctctaaactgttgtgacttgtgtccactttcttgttataaatacaaatatactgtattcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT