Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctgcctgcctctatcctcttttaatttataatccgatggagcaacagtgtatccattgcttgtccgtctgtgagatgcatgcacacagcagccttggcttgaacacttgcttgctttctcctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAGGAGATCATCGAGAGGGCGCACCGCGGCGACATGGACCACGTCAAGCACG

Basic information

species Zea mays
transcript GRMZM2G029087_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029087_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g03280.2 (Oryza sativa), 3'ss of exon 4
gtgcctgcctgcctctatcctcttttaatttataatccgatggagcaacagtgtatccat-tgcttgtccgtctgtgagatgca-tgcacacagcagccttggcttgaacact--tgcttgcttt-ctcctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAGGAGATCATCGAGAGGGCGCACCGCGGCGACATGGACCACGTCAAGCACG
                                          | |  | | ||   | || | |||||||     | | || ||    ||   ||| |||| || ||||||||  | | ||  |   | ||||||||||| ||||| || ||| | ||||||||||| ||| ||||||| |||||||||||||||||||||||||| |||| ||| ||||||||| || |||||||||
------------------------------------------gtgagatactggggctatattcttgtccaatcctaacatacaacatactacgcatcctttgcctgaacactgatacatgtgtggtttctcctgcagGTTTACTTTGGCCTGTTGATCTTCCTGGGGTACATGGTGTATGACACGCAGGAGATCATCGAGAGGGCTCACCACGGTGACATGGACTACATCAAGCACG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|50323899|gb|CO519025.1|CO519025
EST:     TCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: TCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|148964263|gb|EE015455.2|EE015455
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|76288416|gb|DV027984.1|DV027984
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|148965311|gb|EE016118.2|EE016118
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTTCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|148997294|gb|EE035788.2|EE035788
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|51593042|gb|CV072188.1|CV072188
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|149103195|gb|EE288568.2|EE288568
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|76288415|gb|DV027983.1|DV027983
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|76013719|gb|DT940889.1|DT940889
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|47961573|gb|CN844282.1|CN844282
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGACTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|74244275|gb|DT652189.1|DT652189
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|18178570|gb|BM379780.1|BM379780
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|91877668|gb|EB407625.1|EB407625
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACCTCGGGCTGCTCATCTTC
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTC
EST: gi|149008169|gb|EE040357.2|EE040357
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|76013720|gb|DT940890.1|DT940890
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|148954442|gb|EC899865.2|EC899865
EST:     AGCTAGCCGGCTCCTTCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|149048849|gb|EE048352.2|EE048352
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|148954443|gb|EC899866.2|EC899866
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|78105316|gb|DV523734.1|DV523734
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|149108187|gb|EE292532.2|EE292532
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|74232622|gb|DT640536.1|DT640536
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|71432248|gb|DR813298.1|DR813298
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|149110918|gb|EE294416.2|EE294416
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|76011040|gb|DT938210.1|DT938210
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|149008168|gb|EE040356.2|EE040356
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|78110664|gb|DV529067.1|DV529067
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|78110665|gb|DV529068.1|DV529068
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTTCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|149110917|gb|EE294415.2|EE294415
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTGGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|51592969|gb|CV072115.1|CV072115
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|149031748|gb|EE286370.2|EE286370
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|67041238|gb|CO467493.1|CO467493
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|71432249|gb|DR813299.1|DR813299
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|50323900|gb|CO519026.1|CO519026
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|111190431|gb|EE288567.1|EE288567
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTGGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
EST: gi|149046683|gb|EE048073.2|EE048073
EST:     AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAG                         GTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG
genomic: AGCTAGCCGGCTCCATCTTCGGCCACTCCGCAACCAGCTTCATGTTCGAGgtgcctgcct ... cctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatgcacacagcagccttggcttgaacacttgcttgctttctcctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAGGAGATCATCGAGAGGGCGCACCGCGGCGACATGGACCACGTCAAGCACG
                             cacttgcttgctttct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcctgcctgcctctatcctcttttaatttataatccgatggagcaacagtgtatccattgcttgtccgtctgtgagatgcatgcacacagcagccttggcttgaacacttgcttgctttctcctcctgcagGTCTACTTCGGGCTGCTCATCTTCCTGGGCTACGTGGTGTACGACACGCAGGAGATCATCGAGAGGGCGCACCGCGGCGACATGGACCACGTCAAGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA