Sequence
atgc intronic sequence ATGC exonic sequence...tacagtgtcaaattaagataatcgtttgttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
Basic information
species | Glycine max |
transcript | GLYMA10G37520.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 1
tacagtgtcaaattaagataatcgtttgttttccct--tttctggccttagtatcatccttttgcatt--atctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
||| |||| | || || | | | ||| | ||||||| ||| || | ||| | || || |||||| ||| ||||| ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| |||
--tgctgttgaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaataccttgcttcttt--tcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
upper sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g01670.1 (Oryza sativa), 3'ss of exon 1
---tacagtgtcaaattaagataatcgtttgttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatc-cagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
| ||| |||| | | | ||||| || ||| | | | | | | | ||| || | || || | || ||| ||| ||||| ||||| ||||||||||||||||||| |||||| || ||||| || || |||
ttatcttgtggcaaacattacgagtggg--gttttaccacaactgaaa--aatggttccttcctacttattctttgcattctttacttgcttttactataacagGTTTGATCGTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG
upper sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
tacagtgtcaaattaagataatcgtttgttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
| | | || | | | | | || | | | || | | | ||| ||||| || | | ||| ||| | ||| ||||||||||||||||||||||||||||||| |||||| || |||||||| || |||
tttaagggcatttcatacttgtagaatgcctcatgtcacacatctggagcagctttcttacatattatgctataaatccttctttcttttcgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG
upper sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G118693_T02 (Zea mays), 3'ss of exon 1
tacagtgtcaaattaagataatcgtttgttttcccttttctggcct-tagtatcatccttt---tgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
| | ||| | | | | | ||| | || | || || || | ||| ||| ||||||| || || | ||| ||||||||||||||||| ||||| || || |||||||| || ||||| || ||||||
---gttcttgaatccatacactgtcccaaaaaattgtcactgaaatataagaccacatcttgcatgtaatattcatgtgtaaactattttcttttctt-ttcagCTTTGACCGTGACTGGAAGAAGATAGAGGCTTTTGTTGGCTCCAAGACCGTCATCCAG
upper sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 1
--------tacagtgtcaaattaagat-aatcgtttgttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
|||| | | | | ||| | | || | | | || || || | |||||| | ||||| |||| ||| ||| || ||||| | |||||||| ||||||||||| ||| |||| ||||||||||| || |||
gtgatgcgtacaatcttaggcaaggattagacacatgctatatccaggttg--tttggtggtggatct----gatatctcttatgtttgtgttttgattattt---tagGTTTGATAGAGACTGGAAGAAGATTGAAGCTTTTATTGGTTCAAAGACAGTGATTCAG
upper sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
-tacagtgtcaaattaagataatcgttt--gttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
|| || | | | ||| ||| |||| | || | | || | | || || | | |||| ||| | || |||| || ||| ||||||||||| |||||||||||||| |||||||||||||||||||||||||| |||
aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaat-taatggattagtttccataaattgattttgttattgattc--tactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG
upper sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
tacagtgtcaaattaagataatcgtttgttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
| ||| ||| ||| | | || || | | || |||| | | | || | | || | ||||||||| || |||||||||||||||||||| || ||||| || |||||||| || |||
tggagtaggaaaactggattttagaatgcttaagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
ttttcattctttatcc CT-rich tract
ttttgtattttcattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacagtgtcaaattaagataatcgtttgttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
tacagtg
- - - - - - - - - - - - - - - ttccctt
- - - - - - - - - - - - - - - - - - -ttctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg