Sequence
atgc intronic sequence ATGC exonic sequence...gccatattttgcttacagtaggctatagatcttatgcacatgaaaactatgtatagttgaaaatggtctattgctaattcatctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA
Basic information
species | Glycine max |
transcript | GLYMA10G02720.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
gccatattttgcttacagtaggctatagatcttatgcacatgaa-aactatgtatagttgaaaatggtctattgctaattcatctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA
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--gtaatttttcttaccata------agaatttttttacgtgatcaattgtatgctgatgcaagtgcgctaagatgagatagttcacttgcatt----cagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA
upper sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
gccatattttgcttacagtaggctatagatcttatgcacatgaaaactatgtatagttgaaaatggtctattgctaattcatctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACA-AACAGCAA
||||| | | | | | | || | | | | | | || | || ||| || | | | ||||||||| |||||||| ||||| ||||||||||| ||||||||||||||||| ||||| || | || | || |||||| | |||| ||| | |
---gtatttccttcttgccaagtcctctaacacat---cgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG-
upper sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G323936_T01 (Zea mays), 3'ss of exon 3
---------------------------gccatattttgcttacagtaggc-tatagatcttatgcacatgaaaactatgtatagt-tgaaaatgg-------tctattgctaatt---catctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA
| ||| | | | || || || | | ||| |||| | | | | || | || || | ||||| | | | | | | | || ||||||| ||||| || ||||| || |||||||| || ||||| |||||||| ||||||||||| ||| ||| ||| ||| | || | ||| | |||| |
gtagtttactattattgcaggcataggactataggaggtgttccatatgcacatgtacttctcatacaacaaaattgcgagaaatctgtagatcaccctgcttcaacagctaaatttacttttttttgttctatgttagATGTCAGATCCACTGACAGCACTCATGCATGCCGTCCAAGTCATGAACTTTCTCAAGACACTGATCTTGAGGACGCTTCGGGAGCGCGATGATGCAGCCA
upper sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
gccatattttgcttacagtaggctatagatcttatgcacatgaaaactatgtatagttgaa-aatggtctattgctaattcatctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA
| | | | | || || | || ||||| || | || ||| | | | | |||| | | |||| ||||| | ||||| |||| || || |||||||| ||||||||||||||||| || ||||| || |||| |||||||| |||| ||| ||| || |
-----------gtaaaaacaaagt-taacctttgttca-atgaa---taagaatcactgagtagttactaacatttgattcttgcat-tctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA
upper sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
gccatattttgcttacagtaggctataga----tcttatgcacatgaaaactatgtatagttgaaaatggtctattgctaattcatctgtgtctc-ctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA
| | | | || | | |||| | || || || | || | | | | | | | | | ||| | | | |||||||||||||| | || || ||||||||||| ||||||||||||||||| || ||||| || |||| || ||||| || |||| ||| ||| |
----------gttgatattaaatcttgaaaatttcttgttttagctaatgctttg-gtccatggatttcaataaatagaactccttttttgtttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
upper sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S107_15V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------------------gccata--ttttgc---ttacagtaggct-atagatcttatgcacatgaaaactatgta--tagttgaaaatggtctattgctaattcatctgtgtctcctgga--acagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA
||| ||||| ||| || || || || | || | | | ||||| | |||| | | | || || || || || |||||| |||||| ||||| || ||||||||||| ||||||||||||||||| | || || | || | ||| | | || | | ||
gtatagagcacctcttcggtggtctctttcttttgaaactagtttagagctaaaactgtgtagcgtgttgtctcccgtgttttctcatgatctttgcacattatttcagcctcgaaggtcgtttgttgttagttggtgttcgatctgttgacgaaggtcatctctttgataatttgagtttcttgccctgcagATGGTTGATCCGCTAACGGCTCTGATGCATGCCGTTCAAGTGATGAACTTGTTGAAAACTTTGATTCTACGCACATTGAAGGACCGGAAGGCTACTTTGC
upper sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------gccatattttgc-ttacagtaggctatagatcttatgcacatgaaaactatgtatagttgaaaatggtctattgctaatt--catctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA
| | | | || | | | | ||| | || | | | | || |||| | | || || | ||| ||| | | | |||||| ||||||| || ||||| ||||||||||| |||||||| |||||||| ||||| || || || | ||||| | || | | ||
gtatagtgttgtttctacgcttttcacccagagaagctgatgaccattacaagatcagactcgtagagatttcactacagatgctgtcttcgacgtttcatgtgctgaatttgaacgtaggtattccgtgtttatggtgtttcaattgttgtagaatgtgtaacatttattgacattgcttcattatccttcagATGGCTGATCCACTGACAGCTCTGATGCATGCTGTTCAAGTCATGAACTTGCTCAAAACTCTGATTCTTCGCACACTGAAGGACCGAAAGGCCACTTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actatgtatagttgaaaatggtctattgctaattcatctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA
tgctaat putative branch site (score: 2)
tgtctcct putative PPT
ttgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccatattttgcttacagtaggctatagatcttatgcacatgaaaactatgtatagttgaaaatggtctattgctaattcatctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - -tgcttac
- - - - - - - - - - - - - - - - tatgcac
- - - - - - - - - - - - - - - - - - - - - - - ctatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctattgc