Sequence
atgc intronic sequence ATGC exonic sequence...attatttgctttgcattgttccttcacacaacagttctttaccattcttctgttaatagattctggatccatgttcctgataatattgttccattctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCTCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTGGTGCTG
Basic information
| species | Glycine max |
| transcript | GLYMA19G24980.1 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g55010.1 (Oryza sativa), 3'ss of exon 5
--------attatttg-ctttgcattgttccttcacacaacagttctttaccattcttctgttaatagattctggatccatgttcctgataatattgttccattct-cagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCTCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTGGTGCTG
| ||| || || | |||||| | || || | | |||| | ||||| | | |||| || ||| ||||||||| ||||||||||| | ||||| || ||||| ||||| |||||||| ||||| | || ||||||||||| |||||||||||||| ||||| ||||| |
tatcctcgagtataaaatttcacacgcataattcacatattagatcaac-caactcttattttaatccacctt------atgtg---gaaaatgcctttccattctgcagGATCCAGTCCAAAGTAGTGTAACTGTTGGAGTTTCGCACTTTGAGAGATGCTCCCTCTGGGTTCAAGTCTTGTATTACCCATTTTATGGAAGTGGAGGGT
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G060727_T03 (Zea mays), 3'ss of exon 2
attatttgctttgcattgttccttcacacaacagtt-ctttaccattcttctgttaatagattctggatccatgttcctgataata--ttgttccattctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCTCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTGGTGCTG
| ||| | || || || | | || || ||| | || | || | | ||| || | |||| || || || |||||||| || | |||||||| ||||| ||||| || ||||| ||||| | || ||||||||||| ||||||||||| || ||||| |||||||
--aacaaatattggtctatttacaaactaaaaactcactgtagaattatgct-tgggtaaactttggcattattgatcacctaatgcttttttatatctccagGATCCTGTCCAAAGTAGTGTGACTGTTGGAGTTTCACATTTTGAGAGATGCTCGCTCTGGGTTCAAGTTTTGTATTACCCGTTTTATGGAAGTGGTGGAT
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G472770_T02 (Zea mays), 3'ss of exon 3
attatttgctttgcattgttccttcacacaacagtt-ctttaccattcttctgtta--atagattctggatccatgttcctgataatattgttcca--ttctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCTCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTGGTGCTG
||| | || || || | || || || ||| | || || | |||| | | ||| || | ||||||||||| | |||||||| ||||| ||||| || ||||| ||||| | || ||||||||||| ||||||||||| || ||||| ||| |||
-----aaatattggtctatttacaaactaaaaacttactatagaattgtatgcttggggtaaacactggcattactgatcacctaacgcctttttaaccctccagGATCCAGTCCAAAGTAGTGTGACTGTTGGAGTTTCACATTTTGAGAGATGCTCGCTCTGGGTTCAAGTTTTGTATTACCCGTTTTATGGAAGTAGTGGAT
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G01780.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------------------attatttgctttgcattgttccttca----cacaacagttctttaccattcttctgtta-atagattctggatccatgttcctgataatattgttccattctc--agGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCTCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTGGTGCTG
| |||| | | |||| || | | |||||| | || || ||| || || | | | || || || || | | | | ||||||| || |||||||| || |||||||| ||||| ||||||||||||| | | ||||||||||| | || || |||||| |||| | | | |
gttgcatgtcattcttcagtgcttatatactcccatctctttacagttctctaatttcttaagtcttgtcagttggaaaccgtttctgttcttaccaatcaatcagtttcgtatatgttagctgtattatcatggactctgtgatttacttttgtagGATCCTGTACAATGCAGTGTCACCGTTGGTGTGTCCCAATTTGAAAGATGTGGTTTCTGGGTTCAAGTCCTCTACTATCCATTCCGTGGTGCTAGGGGAG
upper sequence: GLYMA19G24980.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0171g00280.t01 (Vitis vinifera), 3'ss of exon 5
attatttgctttgcattgttccttcacacaacagttctttaccattcttctgttaatagattctggat----ccatgttcctgataatattgttccattctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCTCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTGGTGCTG
||| ||||| || || || | | |||| ||| || ||| || ||| ||| | ||| | || | | || ||||||||||| | ||||||||||| |||||||| ||||| ||||| |||||||| ||||||||||| || | ||||| || |||||||| || |||| ||
-agattccatttgctttcttgttttggc--attttcctttgtaatttttacgttg-tactttcatgataagatcttgtgatccgtcatctgttcttgttgctagGATCCAGTGCTCTGCAGTGTGACCGTTGGTGTGTCCCATTTTGAGAGATGTGCCCTTTGGGTTCAGGTCCTATATTATCCCTTCTATGGGAGCGGTGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttctgttaatagattctggatccatgttcctgataatattgttccattctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCTCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTGGTGCTG
tcctgat putative branch site (score: 3)
ttccattctc putative PPT
ataatattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attatttgctttgcattgttccttcacacaacagttctttaccattcttctgttaatagattctggatccatgttcctgataatattgttccattctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCTCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTGGTGCTG
- - - - ctttgca
- - - - - - - - -gttcctt
- - - - - - - - - - - - cacacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttc
