Sequence
atgc intronic sequence ATGC exonic sequencegtaagctttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatcttttataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G47850.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
--gtaagctttgtttccactcat-gtcaaataaaaggctagtct---cgagtttgcat----gatcttt-tataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
|| | | | | | || | | | | | || || | | |||| | ||| || || ||| || ||||||| || || ||||||||||| ||||||| |||||||| |||||||| | || |||||||| |||||||| | | |||| | | | | |
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC------------------------------------------------------------------------------
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
--gtaagc-tttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatctttt---ataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
| || || | | ||| | | | | || | | | || || || || ||||||| || ||||||||||||||| |||| || ||||||||||| |||||| || ||||||||||||||||| | || ||||| | | || | |
gtatgagaattctcctatgattgtgtttcttggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC------------------------------------------------------------------------------
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
----gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagttt---gcatgatcttttataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
| | | | | | | | || | | | ||| | | | || || || || ||||||| || ||||||||||||||| |||| || ||||||||||| |||||| || ||||||||||||||||| | || ||||| | | || | |
gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC------------------------------------------------------------------------------
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G086994_T03 (Zea mays), 3'ss of exon 4
----gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagttt---gcatgatcttttataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
| | | | | | | | || | | | ||| | | | || || || || ||||||| || ||||||||||||||| |||| || ||||||||||| |||||| || ||||||||||||||||| | || ||||| | |
gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCG-------------------------------------------------------------------------------------
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
--------------------gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatcttttataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
|| || || ||| ||| | | | | | | || | || || | | | ||||||| || ||||||||||||||||||||||||||||| ||||||||||||||| | |||||||| ||||||||||| || ||||| || | | |||
gtatgataatgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttg---tttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG------------------------------------------------------------------------------
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G02550.1 (Glycine max), 3'ss of exon 4
--------------gtaagctttgtttccactcatgtcaaataaa--aggctagtctcgagtttgcatgatcttttataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
| || | | |||||| | || | | | | | | || | || || | | | ||||||| || ||||||||||||||||| ||||||||||| ||||||||||||||| | |||||||| ||||||||||| |||||||| || | | |||
gtttgactcttctttttgctcttctgctcgttcatgttacctacaccaaataaatgtaatgattaaaccatgccttttg---tttaaacagGGTGAGAAAGAATGCTCCTACTATTTAAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA------------------------------------------------------------------------------
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G17250.1 (Glycine max), 3'ss of exon 4
--------------gtaagctttgtttccactcatgtcaaata-aaaggctagtctcgagtttgcatgatcttttataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
| || | || ||||| | || | | || | | || | | | | | | | ||||||| || || |||||||||||||||||||||||||| ||||||||||||||| | |||||||| ||||||||||| |||||||| || | | |||
gtatgactcttcgttttgctcttctgctcatccatgttacctacagaaaataatgc--aattggttaaaccatgccttttgtttaaacagGGTGAGAAAGAGTGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA------------------------------------------------------------------------------
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G02540.1 (Glycine max), 3'ss of exon 4
--------------------gtaagctttgtttccactcatgtcaaataaaaggctagtct-cgagtttgcatgatcttttataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
| || || | ||| || || | | || | | | ||| || || || | | | ||| ||| || ||||||||||||||||||||||| ||||| ||||||| ||||||| | |||||||| ||||||||||| || || || || | | |||
gtatgataatggcacttctttttgctcttcttctccctcgcgt-aattgacagcaaattatgcgatgttaagccatgccttttg---tttaaacagGATGAGAAAGAATGCTCCTACTATTTGAAAACAGGGCAGTGCAAATATGGTATATCTTGTAAATTCCATCATCCTCAACCGGCGGGCACATCATTGCCAG------------------------------------------------------------------------------
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0104g01460.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatcttttataaactctttg-tagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
| ||| | ||| | | | ||| | | | || | || || ||| | | ||||||| || ||||||||||||||||||||||||||||| ||||| ||||||||||| |||||||| ||||||||||| || ||||| || | | |||
gttgggatttggtttattcttcaccttttctaatcaaattcgttttactaaatcagcatggttgtaatttggg---aatggacacttccatttagcttatgtttatgaattggaaattttgcaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAGTTTGGTATAACATGTAAATTCCATCATCCTCAACCAGCTGGCACATCATTGCCAG------------------------------------------------------------------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
gtataac putative branch site (score: 3)
tcatcctc putative PPT
taaatttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatcttttataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG