Sequence
atgc intronic sequence ATGC exonic sequence...atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgttgaagatatctaacgtgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGA
Basic information
species | Glycine max |
transcript | GLYMA11G27410.1 |
intron # | 29 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 29
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgttgaagat------atc-taacgtgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGA----------------------
||| | || || | || | | || | | | | | ||| | ||| ||| | | ||| | || | |||| || ||||| | || |||||||| || ||||||||||| ||||| || | ||||| |||||||||||||| ||||| |||||| |
------gtgagaca-acgttttgcattttatatcactgctaccctagagcaccatg-cgcgtattttgcatttttgctcatcatgactgaaaatttttg--ctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGACGCAGTGAACTCCACAGCAGGGATTT
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 29
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 21
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgttgaagatatctaacgtgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGA----------------------
|| | | ||| || || ||| | || ||||| || || | | |||| || | || | || | || || || || || || |||||||| ||||| ||||||||||| ||||||| || || ||||| |||||||||
------------------gtgatgatacatttgactttc-ctcttcttgatcaaatgcga-tatgtctgagctaa-tgatgtgattgttctcatgt--agATGCCACTACACACCATAATCGAGATACAAATGGGCGTCACGGGTGTGGAAGAGAAGAGGTACAAACTCATGGACTGAATGAATACATAAAAGCAGCTGG
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 29
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 22
---------atttttgtggggttcacattgtc----agttggagaaatcttcacttttggtgaatgatgatgaatatgttgaagatatc-taacgtgagatttgtgatttc-cagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGA----------------------
|| | | | | || | || | | |||| | || | || | | | | || |||| | | || || ||| | || ||||| || || || ||||||||||||||||| | ||||| ||||||||| | || ||||| |||||||||
gtaaaatctgaattagaaaatacgagactatcttagaacgattgagctataagctttcagagagtcttggctg-caagccacacacataataacatattttggatgtttcaacagATGCCACTTCACACTATAATAGAGATACAGATGGGAGTTTCTGGTGTGCAAGAGAAACGCTACAAACTCATGGACTGAATTCAAACAACTATTACCACAA
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 29
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 22
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatga--tgat--gaatatgttgaagatatctaacgtgagatttg-tgatt-----tccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGA----------------------
||||| | || | |||| | | || ||| | || || || ||| || | | | || ||||| | ||||| || |||||||| || || |||||||| |||||||| || |||||||||||||||||||| || || |||||||||
----------ttaccacatcattttatgaataaattccttttctaggagaagaaaacaatccaaagttggccaagttacaccctgacaaacttaatgattcacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAAGAGAAAAGATACAAGCTCATGGACTGACTTCGCTTCACAGAATCTTTTG
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 29
lower sequence: EFJ11749 (Selaginella moellendorffii), 3'ss of exon 17
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgttgaagatatctaacgtgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGA
|| ||| | | ||| | | | || || | | | || | |||||| | |||| | |||||||| || || |||||||| |||||||||||| | ||||| |||||||| |||| || || | |
--------------------gtgagtgagtggaatttatctagtcaatatgatctggccaagttccttctttaagcttctgcttcctttgtg--tgccagATGCCTCTTCACACTATCATTGAGATCCAGATGGGAGTCGCAGGTGTACAAGAGAAGCGATACAAGCTCTTATAA---
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 29
lower sequence: EFJ22544 (Selaginella moellendorffii), 3'ss of exon 17
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgttgaagatatctaacgtgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGA
|| ||| | | ||| | | | || || | | | || | |||||| | |||| | |||||||| || || |||||||| |||||||||||| | ||||| |||||||| |||| || || | |
--------------------gtgagtgagtggaatttatctagtcaatatgatctggccaagttccttctttaagcttctgcttcctttgtg--tgccagATGCCTCTTCACACTATCATTGAGATCCAGATGGGAGTCCCAGGTGTACAAGAGAAGCGATACAAGCTCTTATAA--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtgaatgatgatgaatatgttgaagatatctaacgtgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGA
atctaac putative branch site (score: 2)
tttcc putative PPT
atgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgttgaagatatctaacgtgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - ttgtggg
- - - - - - - - - - - - gttggag
- - - - - - - - - - - - - - - - - - - - - - - - - - gatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa